6-118711163-G-C

Variant names:

• chr6-118711163-G-C
• rs794854

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 0.667 in 152,026 control chromosomes in the GnomAD database, including 34,743 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 0.67 (34743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101339 AN: 151912 Hom.: 34719 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.667 AC: 101400 AN: 152026 Hom.: 34743 Cov.: 32 AF XY: 0.656 AC XY: 48720 AN XY: 74304

African (AFR) AF: 0.730 AC: 30276 AN: 41462

American (AMR) AF: 0.572 AC: 8743 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2472 AN: 3464

East Asian (EAS) AF: 0.230 AC: 1191 AN: 5170

South Asian (SAS) AF: 0.496 AC: 2388 AN: 4818

European-Finnish (FIN) AF: 0.612 AC: 6453 AN: 10542

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47555 AN: 67982

Other (OTH) AF: 0.667 AC: 1406 AN: 2108

Alfa AF: 0.592 Hom.: 1860

Bravo AF: 0.666

Asia WGS AF: 0.413 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs794854; hg19: chr6-119032326;