rs2063864

Variant names:

• chr2-145417267-G-A
• rs2063864

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 0.035 in 152,014 control chromosomes in the GnomAD database, including 271 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 0.035 (271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

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 (AFR) allele frequency at 95% confidence interval = 0.112 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: 0.0349 AC: 5294 AN: 151896 Hom.: 269 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0148

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.000851

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00330

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0350 AC: 5317 AN: 152014 Hom.: 271 Cov.: 32 AF XY: 0.0332 AC XY: 2467 AN XY: 74286

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0147

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00175

Gnomad4 SAS AF: 0.00373

Gnomad4 FIN AF: 0.000851

Gnomad4 NFE AF: 0.00330

Gnomad4 OTH AF: 0.0299

Alfa AF: 0.0185 Hom.: 35

Bravo AF: 0.0388

Asia WGS AF: 0.00982 AC: 35 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2063864; hg19: chr2-146174835;