2-136436274-A-T

Position:

• chr2-136436274-A-T

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 0.053 in 151,406 control chromosomes in the GnomAD database, including 565 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 0.053 (565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 7994 AN: 151306 Hom.: 565 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.00895

Gnomad EAS AF: 0.0280

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.000766

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00542

Gnomad OTH AF: 0.0391

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

GnomAD4 genome AF: 0.0530 AC: 8018 AN: 151406 Hom.: 565 Cov.: 32 AF XY: 0.0520 AC XY: 3843 AN XY: 73942

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0287

Gnomad4 ASJ AF: 0.00895

Gnomad4 EAS AF: 0.0283

Gnomad4 SAS AF: 0.0442

Gnomad4 FIN AF: 0.000766

Gnomad4 NFE AF: 0.00543

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0305 Hom.: 28

Bravo AF: 0.0590

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
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: rs10496745; hg19: chr2-137193844;