rs749052

chr2-231931900-T-C

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 0.0732 in 152,212 control chromosomes in the GnomAD database, including 519 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 0.073 (519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 11128 AN: 152094 Hom.: 518 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0792

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

GnomAD4 genome AF: 0.0732 AC: 11139 AN: 152212 Hom.: 519 Cov.: 32 AF XY: 0.0715 AC XY: 5322 AN XY: 74414

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.0779

Alfa AF: 0.0678 Hom.: 841

Bravo AF: 0.0755

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.89
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs749052; hg19: chr2-232796610;