rs2317332

Variant names:

• chr3-101042929-G-A
• rs2317332

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0258 in 152,268 control chromosomes in the GnomAD database, including 80 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 0.026 (80 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0258 (3924/152268) while in subpopulation NFE AF = 0.0435 (2961/68014). AF 95% confidence interval is 0.0422. There are 80 homozygotes in GnomAd4. There are 1784 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 80 gene

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: 0.0258 AC: 3925 AN: 152150 Hom.: 80 Cov.: 32

Gnomad AFR AF: 0.00724

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0258 AC: 3924 AN: 152268 Hom.: 80 Cov.: 32 AF XY: 0.0240 AC XY: 1784 AN XY: 74456

African (AFR) AF: 0.00722 AC: 300 AN: 41562

American (AMR) AF: 0.0169 AC: 259 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4816

European-Finnish (FIN) AF: 0.0135 AC: 143 AN: 10608

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2961 AN: 68014

Other (OTH) AF: 0.0218 AC: 46 AN: 2112

Alfa AF: 0.0376 Hom.: 89

Bravo AF: 0.0255

Asia WGS AF: 0.00751 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.71
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs2317332; hg19: chr3-100761773;