dbSNP rs17501080: ENSG00000300407:n.118-5843A>C (chr7-81774380-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000771413.1(ENSG00000300407):n.118-5843A>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 152,036 control chromosomes in the GnomAD database, including 849 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 ( 849 hom., cov: 32)

Consequence

ENSG00000300407
ENST00000771413.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.586

Publications

1 publications found

Variant links:

Genes affected

ENSG00000300407 (HGNC:):

ENSG00000300407 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300407	ENST00000771413.1 link	n.118-5843A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15719

AN:

151918

Hom.:

848

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0975

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.0696

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.00945

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.0809

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

GnomAD4 genome

AF:

0.103

AC:

15727

AN:

152036

Hom.:

849

Cov.:

AF XY:

0.104

AC XY:

7710

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.0974

AC:

4038

AN:

41464

American (AMR)

AF:

0.0695

AC:

1060

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

400

AN:

3472

East Asian (EAS)

AF:

0.00947

AC:

AN:

5174

South Asian (SAS)

AF:

0.106

AC:

509

AN:

4812

European-Finnish (FIN)

AF:

0.150

AC:

1590

AN:

10572

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.113

AC:

7711

AN:

67984

Other (OTH)

AF:

0.0801

AC:

169

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

705

1411

2116

2822

3527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.121

Hom.:

151

Bravo

AF:

0.0955

Asia WGS

AF:

0.0660

AC:

233

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.9

(source)

DANN

Benign

0.78

PhyloP100

0.59

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