2-136318855-C-T

Variant names:

• chr2-136318855-C-T
• rs4954411

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 0.447 in 151,960 control chromosomes in the GnomAD database, including 17,333 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 0.45 (17333 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.448 AC: 67985 AN: 151840 Hom.: 17340 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.447 AC: 67981 AN: 151960 Hom.: 17333 Cov.: 31 AF XY: 0.441 AC XY: 32753 AN XY: 74234

African (AFR) AF: 0.247 AC: 10232 AN: 41420

American (AMR) AF: 0.390 AC: 5953 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1652 AN: 3472

East Asian (EAS) AF: 0.134 AC: 696 AN: 5188

South Asian (SAS) AF: 0.441 AC: 2131 AN: 4828

European-Finnish (FIN) AF: 0.502 AC: 5289 AN: 10532

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40329 AN: 67940

Other (OTH) AF: 0.443 AC: 936 AN: 2112

Alfa AF: 0.530 Hom.: 28611

Bravo AF: 0.429

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.62
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4954411; hg19: chr2-137076425;