chr2-64313293-G-T

Variant names:

• chr2-64313293-G-T
• rs890478

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 0.536 in 148,428 control chromosomes in the GnomAD database, including 21,540 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 0.54 (21540 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 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: 0.536 AC: 79543 AN: 148324 Hom.: 21518 Cov.: 25

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.536 AC: 79603 AN: 148428 Hom.: 21540 Cov.: 25 AF XY: 0.538 AC XY: 38882 AN XY: 72214

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.488

Alfa AF: 0.503 Hom.: 8136

Bravo AF: 0.522

Asia WGS AF: 0.389 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs890478; hg19: chr2-64540427;