rs17647258

Positions:

• chr6-66414884-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 0.0782 in 151,970 control chromosomes in the GnomAD database, including 662 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 0.078 (662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11893 AN: 151852 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0111

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0788

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

GnomAD4 genome AF: 0.0782 AC: 11889 AN: 151970 Hom.: 662 Cov.: 32 AF XY: 0.0780 AC XY: 5798 AN XY: 74288

Gnomad4 AFR AF: 0.0195

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0111

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0779

Alfa AF: 0.0965 Hom.: 114

Bravo AF: 0.0684

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17647258; hg19: chr6-67124777;