chr2-31450049-T-C

Variant names:

• chr2-31450049-T-C
• rs206793

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 0.0739 in 152,260 control chromosomes in the GnomAD database, including 461 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 0.074 (461 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.108 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: 0.0739 AC: 11240 AN: 152140 Hom.: 461 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0739 AC: 11251 AN: 152260 Hom.: 461 Cov.: 31 AF XY: 0.0735 AC XY: 5471 AN XY: 74460

African (AFR) AF: 0.110 AC: 4585 AN: 41544

American (AMR) AF: 0.0568 AC: 869 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3470

East Asian (EAS) AF: 0.0497 AC: 258 AN: 5186

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4822

European-Finnish (FIN) AF: 0.0664 AC: 705 AN: 10616

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0569 AC: 3873 AN: 68012

Other (OTH) AF: 0.0852 AC: 180 AN: 2112

Alfa AF: 0.0338 Hom.: 29

Bravo AF: 0.0759

Asia WGS AF: 0.0450 AC: 156 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	2.0
DANN	Benign	0.44
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs206793; hg19: chr2-31672915;