2-31517592-C-T

Variant names:

• chr2-31517592-C-T
• rs6732223

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 0.449 in 152,032 control chromosomes in the GnomAD database, including 15,713 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 0.45 (15713 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

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 (NFE) allele frequency at 95% confidence interval = 0.487 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: 0.449 AC: 68220 AN: 151914 Hom.: 15712 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.449 AC: 68232 AN: 152032 Hom.: 15713 Cov.: 33 AF XY: 0.451 AC XY: 33532 AN XY: 74308

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.452

Alfa AF: 0.475 Hom.: 4659

Bravo AF: 0.444

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6732223; hg19: chr2-31742662;