2-21170817-G-T

Variant names:

• chr2-21170817-G-T
• rs488507

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 0.787 in 147,866 control chromosomes in the GnomAD database, including 45,074 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 0.79 (45074 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.787 AC: 116229 AN: 147758 Hom.: 45034 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.787 AC: 116324 AN: 147866 Hom.: 45074 Cov.: 31 AF XY: 0.789 AC XY: 56988 AN XY: 72234

African (AFR) AF: 0.697 AC: 27212 AN: 39062

American (AMR) AF: 0.825 AC: 12358 AN: 14976

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2433 AN: 3388

East Asian (EAS) AF: 0.994 AC: 5145 AN: 5178

South Asian (SAS) AF: 0.861 AC: 4079 AN: 4736

European-Finnish (FIN) AF: 0.787 AC: 8069 AN: 10258

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.811 AC: 54365 AN: 67024

Other (OTH) AF: 0.784 AC: 1606 AN: 2048

Alfa AF: 0.748 Hom.: 4808

Bravo AF: 0.765

Asia WGS AF: 0.919 AC: 3194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.40
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs488507; hg19: chr2-21393689;