4-165583056-T-C

Variant names:

• chr4-165583056-T-C
• rs10517853

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 0.768 in 152,074 control chromosomes in the GnomAD database, including 46,848 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 0.77 (46848 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 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: 0.768 AC: 116703 AN: 151958 Hom.: 46843 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.768 AC: 116742 AN: 152074 Hom.: 46848 Cov.: 31 AF XY: 0.767 AC XY: 57067 AN XY: 74358

African (AFR) AF: 0.508 AC: 21049 AN: 41452

American (AMR) AF: 0.845 AC: 12902 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2740 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3807 AN: 5152

South Asian (SAS) AF: 0.888 AC: 4285 AN: 4826

European-Finnish (FIN) AF: 0.829 AC: 8779 AN: 10592

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60472 AN: 68002

Other (OTH) AF: 0.788 AC: 1661 AN: 2108

Alfa AF: 0.815 Hom.: 6133

Bravo AF: 0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.81
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10517853; hg19: chr4-166504208;