chr3-175812309-T-C

Variant names:

• chr3-175812309-T-C
• rs4386512

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 0.166 in 152,138 control chromosomes in the GnomAD database, including 2,286 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 0.17 (2286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.237 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: 0.166 AC: 25211 AN: 152020 Hom.: 2265 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.166 AC: 25278 AN: 152138 Hom.: 2286 Cov.: 32 AF XY: 0.169 AC XY: 12590 AN XY: 74364

African (AFR) AF: 0.214 AC: 8883 AN: 41528

American (AMR) AF: 0.244 AC: 3717 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3468

East Asian (EAS) AF: 0.134 AC: 691 AN: 5150

South Asian (SAS) AF: 0.178 AC: 862 AN: 4830

European-Finnish (FIN) AF: 0.170 AC: 1801 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8318 AN: 68010

Other (OTH) AF: 0.155 AC: 328 AN: 2110

Alfa AF: 0.140 Hom.: 2464

Bravo AF: 0.174

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.62
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs4386512; hg19: chr3-175530097;