6-93138166-A-T

Position:

• chr6-93138166-A-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93138166A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.857

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs594442; hg19: chr6-93847884;