2-136349177-T-C

Variant names:

• chr2-136349177-T-C
• rs4501004

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.633 in 151,992 control chromosomes in the GnomAD database, including 30,988 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 0.63 (30988 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 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: 0.633 AC: 96179 AN: 151872 Hom.: 30968 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.633 AC: 96233 AN: 151992 Hom.: 30988 Cov.: 31 AF XY: 0.632 AC XY: 46946 AN XY: 74296

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.660

Alfa AF: 0.547 Hom.: 1686

Bravo AF: 0.621

Asia WGS AF: 0.629 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4501004; hg19: chr2-137106747;