2-21176344-G-T

Variant names:

• chr2-21176344-G-T
• rs478442

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 0.766 in 151,914 control chromosomes in the GnomAD database, including 45,061 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 0.77 (45061 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.971
• Publications: 18 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 = 0.971 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: 0.765 AC: 116196 AN: 151796 Hom.: 45021 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.766 AC: 116291 AN: 151914 Hom.: 45061 Cov.: 31 AF XY: 0.767 AC XY: 56946 AN XY: 74254

African (AFR) AF: 0.657 AC: 27195 AN: 41384

American (AMR) AF: 0.810 AC: 12359 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2429 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5123 AN: 5156

South Asian (SAS) AF: 0.846 AC: 4079 AN: 4822

European-Finnish (FIN) AF: 0.763 AC: 8048 AN: 10552

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54392 AN: 67950

Other (OTH) AF: 0.762 AC: 1609 AN: 2112

Alfa AF: 0.764 Hom.: 8354

Bravo AF: 0.765

Asia WGS AF: 0.919 AC: 3194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.52
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs478442; hg19: chr2-21399216;