6-93138166-A-T

Variant names:

• chr6-93138166-A-T
• rs594442

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 0.877 in 151,954 control chromosomes in the GnomAD database, including 58,721 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 0.88 (58721 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 4 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 = 0.937 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133199 AN: 151836 Hom.: 58696 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.877 AC: 133277 AN: 151954 Hom.: 58721 Cov.: 31 AF XY: 0.877 AC XY: 65164 AN XY: 74278

African (AFR) AF: 0.944 AC: 39216 AN: 41522

American (AMR) AF: 0.792 AC: 12054 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2626 AN: 3464

East Asian (EAS) AF: 0.843 AC: 4346 AN: 5156

South Asian (SAS) AF: 0.854 AC: 4127 AN: 4830

European-Finnish (FIN) AF: 0.883 AC: 9356 AN: 10594

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58616 AN: 67862

Other (OTH) AF: 0.857 AC: 1804 AN: 2104

Alfa AF: 0.857 Hom.: 26763

Bravo AF: 0.870

Asia WGS AF: 0.822 AC: 2859 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.47
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs594442; hg19: chr6-93847884;