rs2317332

chr3-101042929-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 80 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00722

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.0382 Hom.: 71

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317332; hg19: chr3-100761773;