3-162043443-T-C

Variant names:

• chr3-162043443-T-C
• rs10513577

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 0.195 in 152,172 control chromosomes in the GnomAD database, including 3,888 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 0.19 (3888 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.195 AC: 29626 AN: 152056 Hom.: 3888 Cov.: 33

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.195 AC: 29621 AN: 152172 Hom.: 3888 Cov.: 33 AF XY: 0.192 AC XY: 14306 AN XY: 74372

African (AFR) AF: 0.0508 AC: 2112 AN: 41564

American (AMR) AF: 0.133 AC: 2025 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3468

East Asian (EAS) AF: 0.00812 AC: 42 AN: 5170

South Asian (SAS) AF: 0.177 AC: 854 AN: 4832

European-Finnish (FIN) AF: 0.325 AC: 3433 AN: 10578

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19914 AN: 67982

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.270 Hom.: 3227

Bravo AF: 0.171

Asia WGS AF: 0.0870 AC: 303 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.70
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs10513577; hg19: chr3-161761231;