6-113158133-G-T

Position:

• chr6-113158133-G-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 0.895 in 152,188 control chromosomes in the GnomAD database, including 61,198 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 0.89 (61198 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113158133G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136089 AN: 152070 Hom.: 61147 Cov.: 33

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.895 AC: 136199 AN: 152188 Hom.: 61198 Cov.: 33 AF XY: 0.892 AC XY: 66380 AN XY: 74388

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.935

Gnomad4 OTH AF: 0.926

Alfa AF: 0.928 Hom.: 57249

Bravo AF: 0.900

Asia WGS AF: 0.853 AC: 2945 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2473967; hg19: chr6-113479335;