dbSNP rs11593057: MSANTD7:c.*2086C>A (chr10-14845980-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001378785.1(MSANTD7):c.*2086C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,688 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
MSANTD7	NM_001378785.1 link	c.*2086C>A	3_prime_UTR_variant	Exon 5 of 5	ENST00000640019.3	NP_001365714.1
HSPA14	NM_016299.4 link	c.222-2629C>A	intron_variant	Intron 3 of 13	ENST00000378372.8	NP_057383.2
MSANTD7	NM_001378790.1 link	c.*2086C>A	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>A	3_prime_UTR_variant	Exon 5 of 5	1	NM_001378785.1	ENSP00000491568.1
HSPA14	ENST00000378372.8 link	c.222-2629C>A	intron_variant	Intron 3 of 13	1	NM_016299.4	ENSP00000367623.3
HSPA14	ENST00000441647.1 link	c.186-2629C>A	intron_variant	Intron 3 of 5	3		ENSP00000404691.1

Frequencies

GnomAD3 genomes

AF:

0.00000659

AC:

AN:

151688

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

778192

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

360858

African (AFR)

AF:

0.00

AC:

AN:

14822

American (AMR)

AF:

0.00

AC:

AN:

926

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4828

East Asian (EAS)

AF:

0.00

AC:

AN:

3442

South Asian (SAS)

AF:

0.00

AC:

AN:

15388

European-Finnish (FIN)

AF:

0.00

AC:

AN:

258

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1504

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

711522

Other (OTH)

AF:

0.00

AC:

AN:

25502

GnomAD4 genome

AF:

0.00000659

AC:

AN:

151688

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74022

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41242

American (AMR)

AF:

0.00

AC:

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10478

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

67940

Other (OTH)

AF:

0.00

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

1117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.86

(source)

DANN

Benign

0.52

PhyloP100

0.023

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over