6-1318643-C-T

Variant names:

• chr6-1318643-C-T
• rs11242675

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 0.583 in 152,230 control chromosomes in the GnomAD database, including 26,302 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 0.58 (26302 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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: 0.583 AC: 88714 AN: 152112 Hom.: 26307 Cov.: 35

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.583 AC: 88738 AN: 152230 Hom.: 26302 Cov.: 35 AF XY: 0.578 AC XY: 43032 AN XY: 74422

African (AFR) AF: 0.514 AC: 21366 AN: 41544

American (AMR) AF: 0.551 AC: 8421 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2637 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2232 AN: 5184

South Asian (SAS) AF: 0.596 AC: 2876 AN: 4824

European-Finnish (FIN) AF: 0.578 AC: 6120 AN: 10580

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43049 AN: 68012

Other (OTH) AF: 0.614 AC: 1299 AN: 2116

Alfa AF: 0.618 Hom.: 107472

Bravo AF: 0.579

Asia WGS AF: 0.501 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.68
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs11242675; hg19: chr6-1318878;