rs2853550

chr2-112829544-A-Gchr2-112829544-A-T

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 0.837 in 152,062 control chromosomes in the GnomAD database, including 54,266 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 0.84 (54266 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 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: 0.837 AC: 127235 AN: 151944 Hom.: 54226 Cov.: 30

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.837 AC: 127322 AN: 152062 Hom.: 54266 Cov.: 30 AF XY: 0.838 AC XY: 62306 AN XY: 74356

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.850

Alfa AF: 0.896 Hom.: 59892

Bravo AF: 0.824

Asia WGS AF: 0.834 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.2
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853550; hg19: chr2-113587121;