rs17178527

Positions:

• chr6-141584943-G-A

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 0.119 in 151,452 control chromosomes in the GnomAD database, including 1,164 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 0.12 (1164 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.141584943G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18043 AN: 151334 Hom.: 1163 Cov.: 32

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0897

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.119 AC: 18043 AN: 151452 Hom.: 1164 Cov.: 32 AF XY: 0.119 AC XY: 8783 AN XY: 74004

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0796

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.119

Alfa AF: 0.122 Hom.: 220

Bravo AF: 0.112

Asia WGS AF: 0.159 AC: 544 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
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: rs17178527; hg19: chr6-141906080; COSMIC: COSV68647625;