2-207627419-A-T

Variant names:

• chr2-207627419-A-T
• rs2551941

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 0.349 in 151,776 control chromosomes in the GnomAD database, including 9,563 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 0.35 (9563 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 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: 0.349 AC: 52949 AN: 151658 Hom.: 9544 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.349 AC: 53004 AN: 151776 Hom.: 9563 Cov.: 31 AF XY: 0.354 AC XY: 26226 AN XY: 74178

African (AFR) AF: 0.304 AC: 12562 AN: 41386

American (AMR) AF: 0.390 AC: 5946 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3472

East Asian (EAS) AF: 0.389 AC: 1999 AN: 5140

South Asian (SAS) AF: 0.512 AC: 2466 AN: 4816

European-Finnish (FIN) AF: 0.386 AC: 4068 AN: 10542

Middle Eastern (MID) AF: 0.295 AC: 85 AN: 288

European-Non Finnish (NFE) AF: 0.351 AC: 23848 AN: 67864

Other (OTH) AF: 0.330 AC: 695 AN: 2108

Alfa AF: 0.344 Hom.: 1129

Bravo AF: 0.349

Asia WGS AF: 0.438 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.70
DANN	Benign	0.71
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2551941; hg19: chr2-208492143;