2-28440466-G-T

Variant names:

• chr2-28440466-G-T
• rs2940787

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 0.539 in 151,988 control chromosomes in the GnomAD database, including 22,830 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 0.54 (22830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81841 AN: 151870 Hom.: 22800 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.539 AC: 81917 AN: 151988 Hom.: 22830 Cov.: 32 AF XY: 0.543 AC XY: 40351 AN XY: 74294

African (AFR) AF: 0.424 AC: 17565 AN: 41434

American (AMR) AF: 0.679 AC: 10371 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2059 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4258 AN: 5164

South Asian (SAS) AF: 0.630 AC: 3035 AN: 4816

European-Finnish (FIN) AF: 0.520 AC: 5488 AN: 10556

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37263 AN: 67950

Other (OTH) AF: 0.581 AC: 1228 AN: 2112

Alfa AF: 0.546 Hom.: 42681

Bravo AF: 0.548

Asia WGS AF: 0.707 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2940787; hg19: chr2-28663333;