chr2-163062630-G-A

Position:

• chr2-163062630-G-A

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 0.336 in 151,718 control chromosomes in the GnomAD database, including 8,916 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 0.34 (8916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.336 AC: 50967 AN: 151600 Hom.: 8883 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.336 AC: 51048 AN: 151718 Hom.: 8916 Cov.: 32 AF XY: 0.342 AC XY: 25330 AN XY: 74120

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.342

Alfa AF: 0.306 Hom.: 915

Bravo AF: 0.342

Asia WGS AF: 0.407 AC: 1412 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	0.33
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1873201; hg19: chr2-163919140;