rs1346822

Variant names:

• chr2-136456791-G-A
• rs1346822

Your query was ambiguous. Multiple possible variants found:

• chr2-136456791-G-A
• chr2-136456791-G-C

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 0.165 in 151,454 control chromosomes in the GnomAD database, including 2,422 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 0.16 (2422 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.164 AC: 24891 AN: 151346 Hom.: 2418 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.165 AC: 24917 AN: 151454 Hom.: 2422 Cov.: 31 AF XY: 0.171 AC XY: 12648 AN XY: 74016

African (AFR) AF: 0.140 AC: 5777 AN: 41314

American (AMR) AF: 0.289 AC: 4398 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 483 AN: 3462

East Asian (EAS) AF: 0.392 AC: 2014 AN: 5132

South Asian (SAS) AF: 0.199 AC: 952 AN: 4792

European-Finnish (FIN) AF: 0.177 AC: 1832 AN: 10356

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.131 AC: 8924 AN: 67870

Other (OTH) AF: 0.179 AC: 376 AN: 2104

Alfa AF: 0.162 Hom.: 848

Bravo AF: 0.176

Asia WGS AF: 0.296 AC: 1029 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.74
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1346822; hg19: chr2-137214361;