chr3-103124186-G-A

Variant names:

• chr3-103124186-G-A
• rs17176829

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 0.337 in 151,780 control chromosomes in the GnomAD database, including 8,686 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 0.34 (8686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 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: 0.337 AC: 51077 AN: 151668 Hom.: 8678 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.337 AC: 51115 AN: 151780 Hom.: 8686 Cov.: 32 AF XY: 0.336 AC XY: 24904 AN XY: 74164

African (AFR) AF: 0.313 AC: 12932 AN: 41356

American (AMR) AF: 0.375 AC: 5727 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2243 AN: 5170

South Asian (SAS) AF: 0.293 AC: 1414 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3035 AN: 10540

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23603 AN: 67850

Other (OTH) AF: 0.328 AC: 690 AN: 2102

Alfa AF: 0.329 Hom.: 1240

Bravo AF: 0.343

Asia WGS AF: 0.360 AC: 1245 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.51
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs17176829; hg19: chr3-102843030;