2-136522811-C-T

Variant names:

• chr2-136522811-C-T
• rs470705

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 0.462 in 151,974 control chromosomes in the GnomAD database, including 18,429 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 0.46 (18429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.67 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: 0.462 AC: 70153 AN: 151856 Hom.: 18372 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.462 AC: 70275 AN: 151974 Hom.: 18429 Cov.: 32 AF XY: 0.468 AC XY: 34793 AN XY: 74276

African (AFR) AF: 0.676 AC: 28051 AN: 41480

American (AMR) AF: 0.488 AC: 7451 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3468

East Asian (EAS) AF: 0.669 AC: 3454 AN: 5164

South Asian (SAS) AF: 0.575 AC: 2769 AN: 4816

European-Finnish (FIN) AF: 0.329 AC: 3472 AN: 10550

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21598 AN: 67918

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.436 Hom.: 3419

Bravo AF: 0.482

Asia WGS AF: 0.649 AC: 2255 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.54
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs470705; hg19: chr2-137280381;