rs6486099

Variant names:

• chr11-13175491-T-C
• rs6486099

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 0.186 in 152,142 control chromosomes in the GnomAD database, including 5,468 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 0.19 (5468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.186 AC: 28282 AN: 152024 Hom.: 5464 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.186 AC: 28310 AN: 152142 Hom.: 5468 Cov.: 32 AF XY: 0.181 AC XY: 13454 AN XY: 74380

African (AFR) AF: 0.495 AC: 20540 AN: 41466

American (AMR) AF: 0.0936 AC: 1432 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3468

East Asian (EAS) AF: 0.0933 AC: 482 AN: 5164

South Asian (SAS) AF: 0.0974 AC: 470 AN: 4826

European-Finnish (FIN) AF: 0.0394 AC: 418 AN: 10612

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0645 AC: 4385 AN: 67992

Other (OTH) AF: 0.151 AC: 320 AN: 2114

Alfa AF: 0.0976 Hom.: 849

Bravo AF: 0.201

Asia WGS AF: 0.108 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs6486099; hg19: chr11-13197038;