Genetic Variant LOC101928849:n.629-14670T>C (chr9-118936436-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001746918.2(LOC101928849):n.629-14670T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,176 control chromosomes in the GnomAD database, including 1,112 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 0.10 ( 1112 hom., cov: 32)

Consequence

LOC101928849
XR_001746918.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336

Publications

3 publications found

Variant links:

Genes affected

LOC101928849 (HGNC:):

LOC101928849 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928849	XR_001746918.2 link	n.629-14670T>C		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15627

AN:

152058

Hom.:

1115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0231

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.313

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.120

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.103

AC:

15627

AN:

152176

Hom.:

1112

Cov.:

AF XY:

0.106

AC XY:

7872

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0230

AC:

956

AN:

41554

American (AMR)

AF:

0.109

AC:

1663

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

716

AN:

3468

East Asian (EAS)

AF:

0.313

AC:

1613

AN:

5146

South Asian (SAS)

AF:

0.209

AC:

1003

AN:

4810

European-Finnish (FIN)

AF:

0.113

AC:

1191

AN:

10586

Middle Eastern (MID)

AF:

0.147

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.120

AC:

8181

AN:

68000

Other (OTH)

AF:

0.120

AC:

253

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

668

1336

2005

2673

3341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.118

Hom.:

2226

Bravo

AF:

0.0975

Asia WGS

AF:

0.208

AC:

724

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.5

(source)

DANN

Benign

0.76

PhyloP100

0.34

Splicing

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