dbSNP rs10499881: ENSG00000301054:n.139-46980C>T (chr7-84613069-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000775795.1(ENSG00000301054):n.139-46980C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 152,108 control chromosomes in the GnomAD database, including 98 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 0.013 ( 98 hom., cov: 32)

Consequence

ENSG00000301054
ENST00000775795.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.96

Publications

0 publications found

Variant links:

COSMIC-nc: COSV70094443

Genes affected

ENSG00000301054 (HGNC:):

ENSG00000301054 links:

Genome browser will be placed here

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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301054	ENST00000775795.1 link	n.139-46980C>T	intron_variant	Intron 2 of 2
ENSG00000301054	ENST00000775796.1 link	n.211+17814C>T	intron_variant	Intron 3 of 3
ENSG00000301054	ENST00000775797.1 link	n.72-46980C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0135

AC:

2057

AN:

151990

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0425

Gnomad ASJ

AF:

0.0193

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.00991

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00412

Gnomad OTH

AF:

0.0167

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

GnomAD4 genome

AF:

0.0135

AC:

2053

AN:

152108

Hom.:

Cov.:

AF XY:

0.0150

AC XY:

1115

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.00164

AC:

AN:

41540

American (AMR)

AF:

0.0424

AC:

646

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.0193

AC:

AN:

3468

East Asian (EAS)

AF:

0.155

AC:

799

AN:

5164

South Asian (SAS)

AF:

0.0106

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00991

AC:

105

AN:

10594

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00412

AC:

280

AN:

67974

Other (OTH)

AF:

0.0161

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

192

288

384

480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<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:

0.00858

Hom.:

Bravo

AF:

0.0168

Asia WGS

AF:

0.0730

AC:

253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.9

(source)

DANN

Benign

0.71

PhyloP100

2.0

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