chr2-136436274-A-T

Variant names:

• chr2-136436274-A-T
• rs10496745

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;