rs2165993

Variant names:

• chr1-211556694-A-G
• rs2165993

Your query was ambiguous. Multiple possible variants found:

• chr1-211556694-A-G
• chr1-211556694-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 0.599 in 152,040 control chromosomes in the GnomAD database, including 28,493 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 0.60 (28493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 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: 0.598 AC: 90919 AN: 151922 Hom.: 28445 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.599 AC: 91029 AN: 152040 Hom.: 28493 Cov.: 32 AF XY: 0.594 AC XY: 44177 AN XY: 74332

African (AFR) AF: 0.793 AC: 32881 AN: 41474

American (AMR) AF: 0.517 AC: 7891 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2205 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2780 AN: 5176

South Asian (SAS) AF: 0.572 AC: 2753 AN: 4814

European-Finnish (FIN) AF: 0.457 AC: 4824 AN: 10546

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35764 AN: 67976

Other (OTH) AF: 0.603 AC: 1275 AN: 2116

Alfa AF: 0.553 Hom.: 72922

Bravo AF: 0.612

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2165993; hg19: chr1-211730036;