chr3-172523969-T-C

Variant names:

• chr3-172523969-T-C
• rs3136586

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 0.178 in 152,134 control chromosomes in the GnomAD database, including 2,974 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 0.18 (2974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 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: 0.178 AC: 27108 AN: 152016 Hom.: 2975 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.178 AC: 27126 AN: 152134 Hom.: 2974 Cov.: 32 AF XY: 0.184 AC XY: 13710 AN XY: 74362

African (AFR) AF: 0.128 AC: 5328 AN: 41536

American (AMR) AF: 0.163 AC: 2489 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2803 AN: 5164

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2342 AN: 10566

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11489 AN: 67972

Other (OTH) AF: 0.178 AC: 376 AN: 2114

Alfa AF: 0.167 Hom.: 410

Bravo AF: 0.170

Asia WGS AF: 0.441 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.62
PromoterAI		-0.0072	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3136586; hg19: chr3-172241759;