2-136353815-T-G

Variant names:

• chr2-136353815-T-G
• rs6743090

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 0.373 in 151,794 control chromosomes in the GnomAD database, including 11,144 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 0.37 (11144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.373 AC: 56508 AN: 151676 Hom.: 11115 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.373 AC: 56579 AN: 151794 Hom.: 11144 Cov.: 32 AF XY: 0.373 AC XY: 27696 AN XY: 74194

African (AFR) AF: 0.504 AC: 20807 AN: 41316

American (AMR) AF: 0.427 AC: 6522 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1888 AN: 5150

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4814

European-Finnish (FIN) AF: 0.348 AC: 3672 AN: 10544

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20278 AN: 67926

Other (OTH) AF: 0.349 AC: 736 AN: 2108

Alfa AF: 0.291 Hom.: 1127

Bravo AF: 0.387

Asia WGS AF: 0.371 AC: 1288 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	0.61
DANN	Benign	0.22
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6743090; hg19: chr2-137111385;