chr2-21170817-G-T

Position:

• chr2-21170817-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.784

Alfa AF: 0.751 Hom.: 4619

Bravo AF: 0.765

Asia WGS AF: 0.919 AC: 3194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488507; hg19: chr2-21393689;