rs9581943

chr13-27919860-G-A

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 0.317 in 152,138 control chromosomes in the GnomAD database, including 8,883 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (8883 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.20

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BP6: Variant 13-27919860-G-A is Benign according to our data. Variant chr13-27919860-G-A is described in ClinVar as [Benign]. Clinvar id is 669733.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 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: 0.317 AC: 48137 AN: 152020 Hom.: 8881 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.317 AC: 48155 AN: 152138 Hom.: 8883 Cov.: 33 AF XY: 0.320 AC XY: 23775 AN XY: 74368

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.330

Alfa AF: 0.388 Hom.: 11516

Bravo AF: 0.293

Asia WGS AF: 0.428 AC: 1487 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

Jun 14, 2018

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	-0.67
Cadd	Benign	19
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9581943; hg19: chr13-28493997;