2-211171950-T-C

Variant names:

• chr2-211171950-T-C
• rs1437933

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 0.734 in 151,820 control chromosomes in the GnomAD database, including 41,186 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 0.73 (41186 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.734 AC: 111319 AN: 151702 Hom.: 41162 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.734 AC: 111398 AN: 151820 Hom.: 41186 Cov.: 31 AF XY: 0.734 AC XY: 54415 AN XY: 74182

African (AFR) AF: 0.799 AC: 33116 AN: 41432

American (AMR) AF: 0.722 AC: 11010 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4281 AN: 5172

South Asian (SAS) AF: 0.663 AC: 3182 AN: 4802

European-Finnish (FIN) AF: 0.723 AC: 7605 AN: 10522

Middle Eastern (MID) AF: 0.667 AC: 192 AN: 288

European-Non Finnish (NFE) AF: 0.702 AC: 47654 AN: 67880

Other (OTH) AF: 0.724 AC: 1524 AN: 2106

Alfa AF: 0.722 Hom.: 6729

Bravo AF: 0.740

Asia WGS AF: 0.749 AC: 2600 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1437933; hg19: chr2-212036675;