rs8071072

Variant names:

• chr17-12665560-A-T
• rs8071072

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: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.16

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;