chr6-17347092-G-C

Position:

• chr6-17347092-G-C

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 0.366 in 152,092 control chromosomes in the GnomAD database, including 11,779 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 0.37 (11779 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17347092G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55571 AN: 151976 Hom.: 11767 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.366 AC: 55598 AN: 152092 Hom.: 11779 Cov.: 32 AF XY: 0.372 AC XY: 27629 AN XY: 74348

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.389

Alfa AF: 0.237 Hom.: 558

Bravo AF: 0.361

Asia WGS AF: 0.515 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2066272; hg19: chr6-17347323;