rs1356056

Variant names:

• chr2-169376343-T-C
• rs1356056

Your query was ambiguous. Multiple possible variants found:

• chr2-169376343-T-C
• chr2-169376343-T-G

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 0.418 in 151,998 control chromosomes in the GnomAD database, including 13,657 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 0.42 (13657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 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: 0.418 AC: 63526 AN: 151880 Hom.: 13650 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.418 AC: 63556 AN: 151998 Hom.: 13657 Cov.: 32 AF XY: 0.420 AC XY: 31215 AN XY: 74278

African (AFR) AF: 0.426 AC: 17630 AN: 41410

American (AMR) AF: 0.343 AC: 5243 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3755 AN: 5170

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4818

European-Finnish (FIN) AF: 0.443 AC: 4668 AN: 10548

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27630 AN: 67998

Other (OTH) AF: 0.413 AC: 873 AN: 2114

Alfa AF: 0.402 Hom.: 7407

Bravo AF: 0.416

Asia WGS AF: 0.520 AC: 1809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.84
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1356056; hg19: chr2-170232853;