4-65718188-T-C

Variant names:

• chr4-65718188-T-C
• rs4629506

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 0.69 in 151,626 control chromosomes in the GnomAD database, including 38,021 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 (38021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 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: 0.690 AC: 104578 AN: 151508 Hom.: 38026 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.690 AC: 104603 AN: 151626 Hom.: 38021 Cov.: 31 AF XY: 0.695 AC XY: 51487 AN XY: 74086

African (AFR) AF: 0.436 AC: 18038 AN: 41384

American (AMR) AF: 0.767 AC: 11630 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2463 AN: 3462

East Asian (EAS) AF: 0.896 AC: 4574 AN: 5106

South Asian (SAS) AF: 0.782 AC: 3771 AN: 4822

European-Finnish (FIN) AF: 0.797 AC: 8421 AN: 10562

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53163 AN: 67830

Other (OTH) AF: 0.711 AC: 1492 AN: 2098

Alfa AF: 0.755 Hom.: 181827

Bravo AF: 0.676

Asia WGS AF: 0.804 AC: 2794 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4629506; hg19: chr4-66583906;