6-130466631-C-T

Variant names:

• chr6-130466631-C-T
• rs11751990

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 0.105 in 152,054 control chromosomes in the GnomAD database, including 1,021 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 0.11 (1021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 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: 0.105 AC: 16012 AN: 151936 Hom.: 1020 Cov.: 32

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.105 AC: 16021 AN: 152054 Hom.: 1021 Cov.: 32 AF XY: 0.106 AC XY: 7914 AN XY: 74314

African (AFR) AF: 0.0546 AC: 2265 AN: 41476

American (AMR) AF: 0.164 AC: 2497 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3472

East Asian (EAS) AF: 0.0551 AC: 286 AN: 5188

South Asian (SAS) AF: 0.108 AC: 521 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1283 AN: 10540

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8359 AN: 67972

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

Alfa AF: 0.118 Hom.: 3202

Bravo AF: 0.104

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.025
DANN	Benign	0.18
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs11751990; hg19: chr6-130787776;