rs2366956

Variant names:

• chr2-85942658-G-A
• rs2366956

Your query was ambiguous. Multiple possible variants found:

• chr2-85942658-G-A
• chr2-85942658-G-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 0.376 in 152,142 control chromosomes in the GnomAD database, including 13,315 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 0.38 (13315 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57195 AN: 152024 Hom.: 13319 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.376 AC: 57175 AN: 152142 Hom.: 13315 Cov.: 33 AF XY: 0.373 AC XY: 27709 AN XY: 74368

African (AFR) AF: 0.120 AC: 4992 AN: 41544

American (AMR) AF: 0.354 AC: 5413 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1739 AN: 3468

East Asian (EAS) AF: 0.122 AC: 633 AN: 5180

South Asian (SAS) AF: 0.403 AC: 1939 AN: 4816

European-Finnish (FIN) AF: 0.465 AC: 4905 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36012 AN: 67966

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

Alfa AF: 0.346 Hom.: 1189

Bravo AF: 0.351

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.41
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2366956; hg19: chr2-86169781;