4-4877046-C-T

Variant names:

• chr4-4877046-C-T
• rs4689955

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 0.598 in 151,906 control chromosomes in the GnomAD database, including 27,707 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 0.60 (27707 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.598 AC: 90796 AN: 151788 Hom.: 27656 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.598 AC: 90904 AN: 151906 Hom.: 27707 Cov.: 31 AF XY: 0.608 AC XY: 45116 AN XY: 74250

African (AFR) AF: 0.670 AC: 27766 AN: 41428

American (AMR) AF: 0.576 AC: 8800 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2234 AN: 3472

East Asian (EAS) AF: 0.804 AC: 4151 AN: 5166

South Asian (SAS) AF: 0.681 AC: 3268 AN: 4802

European-Finnish (FIN) AF: 0.668 AC: 7031 AN: 10522

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35906 AN: 67936

Other (OTH) AF: 0.573 AC: 1208 AN: 2108

Alfa AF: 0.562 Hom.: 4932

Bravo AF: 0.588

Asia WGS AF: 0.711 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4689955; hg19: chr4-4878773;