chr2-644953-A-G

Position:

• chr2-644953-A-G

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 0.817 in 152,184 control chromosomes in the GnomAD database, including 50,952 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 0.82 (50952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.817 AC: 124264 AN: 152066 Hom.: 50931 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.817 AC: 124340 AN: 152184 Hom.: 50952 Cov.: 33 AF XY: 0.821 AC XY: 61067 AN XY: 74422

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.827

Alfa AF: 0.822 Hom.: 71868

Bravo AF: 0.814

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7561317; hg19: chr2-644953;