chr2-136649442-T-C

Variant names:

• chr2-136649442-T-C
• rs6711718

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 0.541 in 151,992 control chromosomes in the GnomAD database, including 22,875 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 0.54 (22875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 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: 0.541 AC: 82218 AN: 151874 Hom.: 22869 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.541 AC: 82269 AN: 151992 Hom.: 22875 Cov.: 32 AF XY: 0.534 AC XY: 39673 AN XY: 74244

African (AFR) AF: 0.550 AC: 22814 AN: 41470

American (AMR) AF: 0.563 AC: 8593 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3468

East Asian (EAS) AF: 0.193 AC: 997 AN: 5162

South Asian (SAS) AF: 0.454 AC: 2180 AN: 4806

European-Finnish (FIN) AF: 0.478 AC: 5041 AN: 10552

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38518 AN: 67940

Other (OTH) AF: 0.581 AC: 1228 AN: 2114

Alfa AF: 0.563 Hom.: 13619

Bravo AF: 0.548

Asia WGS AF: 0.341 AC: 1185 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.092
DANN	Benign	0.67
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6711718; hg19: chr2-137407012;