2-215439661-T-C

Variant names:

• chr2-215439661-T-C
• rs1250229

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 0.77 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
• Publications: 73 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.812 AC: 33613 AN: 41406

American (AMR) AF: 0.773 AC: 11787 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2695 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4759 AN: 5160

South Asian (SAS) AF: 0.570 AC: 2725 AN: 4778

European-Finnish (FIN) AF: 0.812 AC: 8570 AN: 10552

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50257 AN: 67960

Other (OTH) AF: 0.778 AC: 1638 AN: 2106

Alfa AF: 0.754 Hom.: 114939

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1250229; hg19: chr2-216304384;