6-115043324-C-T

Variant names:

• chr6-115043324-C-T
• rs238590

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 0.723 in 152,038 control chromosomes in the GnomAD database, including 41,226 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 0.72 (41226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 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: 0.722 AC: 109756 AN: 151920 Hom.: 41170 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.723 AC: 109872 AN: 152038 Hom.: 41226 Cov.: 31 AF XY: 0.717 AC XY: 53267 AN XY: 74296

African (AFR) AF: 0.932 AC: 38698 AN: 41502

American (AMR) AF: 0.625 AC: 9545 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2690 AN: 5142

South Asian (SAS) AF: 0.745 AC: 3598 AN: 4828

European-Finnish (FIN) AF: 0.622 AC: 6552 AN: 10532

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44326 AN: 67960

Other (OTH) AF: 0.680 AC: 1438 AN: 2114

Alfa AF: 0.701 Hom.: 5564

Bravo AF: 0.729

Asia WGS AF: 0.689 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.75
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs238590; hg19: chr6-115364488;