Genetic Variant MSANTD7:c.*2086C>T (chr10-14845980-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001378785.1(MSANTD7):c.*2086C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 922,844 control chromosomes in the GnomAD database, including 9,028 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1118 hom., cov: 32)

Exomes 𝑓: 0.14 ( 7910 hom. )

Consequence

MSANTD7
NM_001378785.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0230

Publications

4 publications found

Variant links:

Genes affected

MSANTD7 (HGNC:56248): (Myb/SANT DNA binding domain containing 7)

MSANTD7 links:

HSPA14 (HGNC:29526): (heat shock protein family A (Hsp70) member 14) Predicted to enable several functions, including ATP binding activity; misfolded protein binding activity; and unfolded protein binding activity. Predicted to be involved in several processes, including cellular response to unfolded protein; chaperone cofactor-dependent protein refolding; and protein refolding. Located in cytosol. Colocalizes with ribosome. [provided by Alliance of Genome Resources, Apr 2022]

HSPA14 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
MSANTD7	NM_001378785.1 link	c.*2086C>T	3_prime_UTR_variant	Exon 5 of 5	ENST00000640019.3	NP_001365714.1
HSPA14	NM_016299.4 link	c.222-2629C>T	intron_variant	Intron 3 of 13	ENST00000378372.8	NP_057383.2
MSANTD7	NM_001378790.1 link	c.*2086C>T	3_prime_UTR_variant	Exon 4 of 4		NP_001365719.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
MSANTD7	ENST00000640019.3 link	c.*2086C>T	3_prime_UTR_variant	Exon 5 of 5	1	NM_001378785.1	ENSP00000491568.1
HSPA14	ENST00000378372.8 link	c.222-2629C>T	intron_variant	Intron 3 of 13	1	NM_016299.4	ENSP00000367623.3
HSPA14	ENST00000441647.1 link	c.186-2629C>T	intron_variant	Intron 3 of 5	3		ENSP00000404691.1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16242

AN:

151656

Hom.:

1118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0306

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.00309

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.141

AC:

108439

AN:

771070

Hom.:

7910

Cov.:

AF XY:

0.141

AC XY:

50512

AN XY:

357544

show subpopulations

African (AFR)

AF:

0.0197

AC:

292

AN:

14800

American (AMR)

AF:

0.115

AC:

105

AN:

912

Ashkenazi Jewish (ASJ)

AF:

0.0836

AC:

401

AN:

4794

East Asian (EAS)

AF:

0.00494

AC:

AN:

3442

South Asian (SAS)

AF:

0.0984

AC:

1504

AN:

15286

European-Finnish (FIN)

AF:

0.111

AC:

AN:

252

Middle Eastern (MID)

AF:

0.144

AC:

214

AN:

1490

European-Non Finnish (NFE)

AF:

0.146

AC:

102673

AN:

704806

Other (OTH)

AF:

0.127

AC:

3205

AN:

25288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

3583

7166

10748

14331

17914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4948

9896

14844

19792

24740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.107

AC:

16243

AN:

151774

Hom.:

1118

Cov.:

AF XY:

0.107

AC XY:

7956

AN XY:

74122

show subpopulations

African (AFR)

AF:

0.0306

AC:

1267

AN:

41360

American (AMR)

AF:

0.112

AC:

1703

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

347

AN:

3466

East Asian (EAS)

AF:

0.00309

AC:

AN:

5170

South Asian (SAS)

AF:

0.101

AC:

485

AN:

4806

European-Finnish (FIN)

AF:

0.152

AC:

1595

AN:

10474

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.154

AC:

10450

AN:

67918

Other (OTH)

AF:

0.106

AC:

224

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

727

1455

2182

2910

3637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.127

Hom.:

1117

Bravo

AF:

0.0997

Asia WGS

AF:

0.0520

AC:

180

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.61

PhyloP100

0.023

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over