17-12665560-A-T

Variant names:

• chr17-12665560-A-T
• rs8071072

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.675 AC: 28011 AN: 41484

American (AMR) AF: 0.357 AC: 5452 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1260 AN: 5062

South Asian (SAS) AF: 0.209 AC: 1004 AN: 4810

European-Finnish (FIN) AF: 0.291 AC: 3079 AN: 10576

Middle Eastern (MID) AF: 0.293 AC: 85 AN: 290

European-Non Finnish (NFE) AF: 0.247 AC: 16756 AN: 67880

Other (OTH) AF: 0.346 AC: 730 AN: 2108

Alfa AF: 0.315 Hom.: 1255

Bravo AF: 0.401

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.9
DANN	Benign	0.84
PhyloP100		-4.2
PromoterAI		0.0097	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

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