chr13-20193129-T-C

Position:

• chr13-20193129-T-C

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 0.804 in 144,002 control chromosomes in the GnomAD database, including 50,782 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.80 (50766 hom., cov: 21)
  • Exomes 𝑓: 0.92 (16 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 13-20193129-T-C is Benign according to our data. Variant chr13-20193129-T-C is described in ClinVar as [Benign]. Clinvar id is 1242260.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.804 AC: 115774 AN: 143910 Hom.: 50769 Cov.: 21

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.830

GnomAD4 exome AF: 0.917 AC: 33 AN: 36 Hom.: 16 AF XY: 0.923 AC XY: 24 AN XY: 26

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.969

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.804 AC: 115787 AN: 143966 Hom.: 50766 Cov.: 21 AF XY: 0.809 AC XY: 56941 AN XY: 70406

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.959

Gnomad4 OTH AF: 0.832

Alfa AF: 0.856 Hom.: 6897

Bravo AF: 0.753

Asia WGS AF: 0.938 AC: 3247 AN: 3462

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	-0.90
CADD	Benign	4.7
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9552101; hg19: chr13-20767268;