2-215439661-T-C

Variant names:

• chr2-215439661-T-C
• rs1250229

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;