chr6-130645656-C-T

Variant names:

• chr6-130645656-C-T
• rs2136055

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 0.418 in 151,952 control chromosomes in the GnomAD database, including 15,722 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 0.42 (15722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.85
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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: 0.418 AC: 63412 AN: 151836 Hom.: 15698 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.418 AC: 63486 AN: 151952 Hom.: 15722 Cov.: 32 AF XY: 0.420 AC XY: 31184 AN XY: 74280

African (AFR) AF: 0.638 AC: 26447 AN: 41440

American (AMR) AF: 0.451 AC: 6893 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3470

East Asian (EAS) AF: 0.722 AC: 3725 AN: 5156

South Asian (SAS) AF: 0.583 AC: 2811 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2052 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19166 AN: 67928

Other (OTH) AF: 0.427 AC: 902 AN: 2110

Alfa AF: 0.356 Hom.: 20332

Bravo AF: 0.442

Asia WGS AF: 0.666 AC: 2313 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.59
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs2136055; hg19: chr6-130966801;