rs8071072

Positions:

• chr17-12665560-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.379 in 151,880 control chromosomes in the GnomAD database, including 13,471 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.38 (13471 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 17-12665560-A-T is Benign according to our data. Variant chr17-12665560-A-T is described in ClinVar as [Benign]. Clinvar id is 1289485.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12665560A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57401 AN: 151762 Hom.: 13423 Cov.: 33

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.379 AC: 57511 AN: 151880 Hom.: 13471 Cov.: 33 AF XY: 0.377 AC XY: 27942 AN XY: 74212

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.346

Alfa AF: 0.315 Hom.: 1255

Bravo AF: 0.401

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8071072; hg19: chr17-12568877; COSMIC: COSV58510511;