2-31330683-G-C

Variant names:

• chr2-31330683-G-C
• rs10490361

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 0.391 in 152,094 control chromosomes in the GnomAD database, including 13,099 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 0.39 (13099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 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: 0.391 AC: 59454 AN: 151974 Hom.: 13098 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.391 AC: 59469 AN: 152094 Hom.: 13099 Cov.: 32 AF XY: 0.399 AC XY: 29684 AN XY: 74330

African (AFR) AF: 0.182 AC: 7558 AN: 41496

American (AMR) AF: 0.525 AC: 8023 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2859 AN: 5168

South Asian (SAS) AF: 0.479 AC: 2312 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5661 AN: 10558

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30370 AN: 67978

Other (OTH) AF: 0.396 AC: 836 AN: 2112

Alfa AF: 0.301 Hom.: 884

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.71
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10490361; hg19: chr2-31553549;