2-62663416-T-C

Position:

• chr2-62663416-T-C

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 0.693 in 152,082 control chromosomes in the GnomAD database, including 36,816 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 0.69 (36816 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105257 AN: 151964 Hom.: 36786 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.693 AC: 105339 AN: 152082 Hom.: 36816 Cov.: 33 AF XY: 0.690 AC XY: 51289 AN XY: 74318

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.679

Alfa AF: 0.661 Hom.: 18937

Bravo AF: 0.700

Asia WGS AF: 0.748 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1487074; hg19: chr2-62890551;