6-160293044-T-G

Position:

• chr6-160293044-T-G

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 0.275 in 152,030 control chromosomes in the GnomAD database, including 5,836 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 0.28 (5836 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.160293044T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41760 AN: 151912 Hom.: 5818 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.275 AC: 41815 AN: 152030 Hom.: 5836 Cov.: 33 AF XY: 0.278 AC XY: 20663 AN XY: 74308

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.263

Alfa AF: 0.269 Hom.: 897

Bravo AF: 0.277

Asia WGS AF: 0.254 AC: 879 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2504954; hg19: chr6-160714076;