2-638144-G-T

Variant names:

• chr2-638144-G-T
• rs4854344

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 0.822 in 152,204 control chromosomes in the GnomAD database, including 51,592 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 0.82 (51592 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 49 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 = 0.897 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: 0.822 AC: 125059 AN: 152086 Hom.: 51568 Cov.: 33

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.822 AC: 125140 AN: 152204 Hom.: 51592 Cov.: 33 AF XY: 0.826 AC XY: 61462 AN XY: 74416

African (AFR) AF: 0.784 AC: 32550 AN: 41518

American (AMR) AF: 0.859 AC: 13138 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2549 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4753 AN: 5174

South Asian (SAS) AF: 0.859 AC: 4151 AN: 4830

European-Finnish (FIN) AF: 0.849 AC: 9000 AN: 10606

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56289 AN: 67996

Other (OTH) AF: 0.827 AC: 1749 AN: 2114

Alfa AF: 0.821 Hom.: 149946

Bravo AF: 0.820

Asia WGS AF: 0.883 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.62
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4854344; hg19: chr2-638144;