6-121460244-T-C

Variant names:

• chr6-121460244-T-C
• rs11154027

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 0.61 in 151,882 control chromosomes in the GnomAD database, including 28,872 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 0.61 (28872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.610 AC: 92619 AN: 151764 Hom.: 28842 Cov.: 31

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.610 AC: 92696 AN: 151882 Hom.: 28872 Cov.: 31 AF XY: 0.614 AC XY: 45584 AN XY: 74246

African (AFR) AF: 0.728 AC: 30159 AN: 41450

American (AMR) AF: 0.666 AC: 10155 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1972 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2841 AN: 5164

South Asian (SAS) AF: 0.548 AC: 2638 AN: 4812

European-Finnish (FIN) AF: 0.579 AC: 6085 AN: 10518

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37061 AN: 67914

Other (OTH) AF: 0.587 AC: 1237 AN: 2108

Alfa AF: 0.576 Hom.: 41530

Bravo AF: 0.622

Asia WGS AF: 0.546 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.88
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs11154027; hg19: chr6-121781390;