4-10274358-A-G

Variant names:

• chr4-10274358-A-G
• rs6833142

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.689 in 151,968 control chromosomes in the GnomAD database, including 36,280 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 0.69 (36280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.62
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 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

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104672 AN: 151850 Hom.: 36250 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.689 AC: 104751 AN: 151968 Hom.: 36280 Cov.: 31 AF XY: 0.687 AC XY: 51018 AN XY: 74254

African (AFR) AF: 0.687 AC: 28487 AN: 41456

American (AMR) AF: 0.691 AC: 10534 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2756 AN: 3466

East Asian (EAS) AF: 0.506 AC: 2607 AN: 5148

South Asian (SAS) AF: 0.725 AC: 3484 AN: 4804

European-Finnish (FIN) AF: 0.655 AC: 6911 AN: 10556

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47660 AN: 67968

Other (OTH) AF: 0.706 AC: 1493 AN: 2114

Alfa AF: 0.695 Hom.: 20033

Bravo AF: 0.693

Asia WGS AF: 0.629 AC: 2185 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.011
DANN	Benign	0.23
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs6833142; hg19: chr4-10275982;