rs13023983

Variant names:

• chr2-163334132-A-C
• rs13023983

Your query was ambiguous. Multiple possible variants found:

• chr2-163334132-A-C
• chr2-163334132-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 0.17 in 151,850 control chromosomes in the GnomAD database, including 2,424 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 0.17 (2424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 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: 0.170 AC: 25778 AN: 151732 Hom.: 2420 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0574

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.170 AC: 25798 AN: 151850 Hom.: 2424 Cov.: 32 AF XY: 0.164 AC XY: 12148 AN XY: 74230

African (AFR) AF: 0.179 AC: 7401 AN: 41462

American (AMR) AF: 0.138 AC: 2098 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5170

South Asian (SAS) AF: 0.0577 AC: 278 AN: 4820

European-Finnish (FIN) AF: 0.152 AC: 1613 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13200 AN: 67820

Other (OTH) AF: 0.184 AC: 387 AN: 2108

Alfa AF: 0.177 Hom.: 3168

Bravo AF: 0.171

Asia WGS AF: 0.0440 AC: 152 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs13023983; hg19: chr2-164190642;