rs1250229

chr2-215439661-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 0.77 in 151,896 control chromosomes in the GnomAD database, including 45,335 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 0.77 (45335 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.770 AC: 116920 AN: 151778 Hom.: 45305 Cov.: 29

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.770 AC: 117002 AN: 151896 Hom.: 45335 Cov.: 29 AF XY: 0.773 AC XY: 57359 AN XY: 74214

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.778

Alfa AF: 0.758 Hom.: 4200

Bravo AF: 0.774

Asia WGS AF: 0.701 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1250229; hg19: chr2-216304384;