17-13018328-T-C

Variant names:

• chr17-13018328-T-C
• rs2051974

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 0.729 in 289,472 control chromosomes in the GnomAD database, including 78,235 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.71 (39008 hom., cov: 34)
  • Exomes 𝑓: 0.75 (39227 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.892
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 17-13018328-T-C is Benign according to our data. Variant chr17-13018328-T-C is described in ClinVar as Benign. ClinVar VariationId is 683498.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.710 AC: 108025 AN: 152054 Hom.: 39009 Cov.: 34

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.733

GnomAD4 exome AF: 0.749 AC: 102843 AN: 137300 Hom.: 39227 AF XY: 0.744 AC XY: 52452 AN XY: 70510

African (AFR) AF: 0.549 AC: 1896 AN: 3452

American (AMR) AF: 0.769 AC: 3227 AN: 4198

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 3741 AN: 4748

East Asian (EAS) AF: 0.885 AC: 8285 AN: 9362

South Asian (SAS) AF: 0.674 AC: 9925 AN: 14736

European-Finnish (FIN) AF: 0.785 AC: 5566 AN: 7090

Middle Eastern (MID) AF: 0.728 AC: 450 AN: 618

European-Non Finnish (NFE) AF: 0.749 AC: 63082 AN: 84208

Other (OTH) AF: 0.751 AC: 6671 AN: 8888

GnomAD4 genome AF: 0.710 AC: 108064 AN: 152172 Hom.: 39008 Cov.: 34 AF XY: 0.714 AC XY: 53084 AN XY: 74392

African (AFR) AF: 0.558 AC: 23155 AN: 41486

American (AMR) AF: 0.757 AC: 11579 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2764 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4699 AN: 5176

South Asian (SAS) AF: 0.689 AC: 3320 AN: 4822

European-Finnish (FIN) AF: 0.800 AC: 8490 AN: 10616

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51573 AN: 67988

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.746 Hom.: 22606

Bravo AF: 0.705

Asia WGS AF: 0.776 AC: 2701 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		-0.89
PromoterAI		0.0065	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2051974; hg19: chr17-12921645;