4-107478889-G-C

Variant names:

• chr4-107478889-G-C
• rs4956103

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 0.734 in 151,884 control chromosomes in the GnomAD database, including 41,038 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 0.73 (41038 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.791 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: 0.734 AC: 111370 AN: 151768 Hom.: 40994 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.734 AC: 111473 AN: 151884 Hom.: 41038 Cov.: 30 AF XY: 0.735 AC XY: 54507 AN XY: 74178

African (AFR) AF: 0.798 AC: 33053 AN: 41418

American (AMR) AF: 0.720 AC: 11002 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4147 AN: 5132

South Asian (SAS) AF: 0.810 AC: 3888 AN: 4798

European-Finnish (FIN) AF: 0.695 AC: 7327 AN: 10548

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.697 AC: 47321 AN: 67928

Other (OTH) AF: 0.735 AC: 1554 AN: 2114

Alfa AF: 0.608 Hom.: 1680

Bravo AF: 0.736

Asia WGS AF: 0.831 AC: 2887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4956103; hg19: chr4-108400046;