chr3-172454579-G-A

Variant names:

• chr3-172454579-G-A
• rs11918879

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 0.316 in 151,970 control chromosomes in the GnomAD database, including 7,706 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 0.32 (7706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 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: 0.316 AC: 48008 AN: 151852 Hom.: 7698 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.316 AC: 48047 AN: 151970 Hom.: 7706 Cov.: 32 AF XY: 0.323 AC XY: 23968 AN XY: 74286

African (AFR) AF: 0.328 AC: 13598 AN: 41440

American (AMR) AF: 0.307 AC: 4692 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1895 AN: 5168

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4816

European-Finnish (FIN) AF: 0.377 AC: 3983 AN: 10552

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19420 AN: 67940

Other (OTH) AF: 0.311 AC: 656 AN: 2106

Alfa AF: 0.296 Hom.: 1384

Bravo AF: 0.308

Asia WGS AF: 0.425 AC: 1471 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs11918879; hg19: chr3-172172369;