2-64363312-C-G

Variant names:

• chr2-64363312-C-G
• rs872683

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.12 in 152,134 control chromosomes in the GnomAD database, including 1,115 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 0.12 (1115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.126 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: 0.120 AC: 18207 AN: 152016 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.120 AC: 18248 AN: 152134 Hom.: 1115 Cov.: 32 AF XY: 0.120 AC XY: 8909 AN XY: 74378

African (AFR) AF: 0.122 AC: 5059 AN: 41482

American (AMR) AF: 0.131 AC: 1998 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3472

East Asian (EAS) AF: 0.0738 AC: 383 AN: 5190

South Asian (SAS) AF: 0.105 AC: 506 AN: 4816

European-Finnish (FIN) AF: 0.159 AC: 1690 AN: 10596

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8014 AN: 67986

Other (OTH) AF: 0.110 AC: 232 AN: 2114

Alfa AF: 0.0553 Hom.: 71

Bravo AF: 0.118

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.71
DANN	Benign	0.37
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs872683; hg19: chr2-64590446;