rs3923113

Variant names:

• chr2-164645339-A-C
• rs3923113

Your query was ambiguous. Multiple possible variants found:

• chr2-164645339-A-C
• chr2-164645339-A-G
• chr2-164645339-A-T

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 0.429 in 152,044 control chromosomes in the GnomAD database, including 16,111 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 0.43 (16111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 101 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 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: 0.429 AC: 65195 AN: 151926 Hom.: 16068 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.429 AC: 65277 AN: 152044 Hom.: 16111 Cov.: 32 AF XY: 0.421 AC XY: 31327 AN XY: 74334

African (AFR) AF: 0.687 AC: 28446 AN: 41432

American (AMR) AF: 0.304 AC: 4651 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1077 AN: 3472

East Asian (EAS) AF: 0.125 AC: 646 AN: 5170

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3360 AN: 10568

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

European-Non Finnish (NFE) AF: 0.363 AC: 24684 AN: 67990

Other (OTH) AF: 0.393 AC: 829 AN: 2112

Alfa AF: 0.374 Hom.: 38817

Bravo AF: 0.442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.2
DANN	Benign	0.85
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs3923113; hg19: chr2-165501849;