rs561241

Positions:

• chr13-113105720-T-C
• chr13-113105720-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.126 in 1,145,320 control chromosomes in the GnomAD database, including 10,679 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.12 (1257 hom., cov: 31)
  • Exomes 𝑓: 0.13 (9422 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 13-113105720-T-C is Benign according to our data. Variant chr13-113105720-T-C is described in ClinVar as [Benign]. Clinvar id is 1249500.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113105720T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18803 AN: 152062 Hom.: 1256 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.127 AC: 125838 AN: 993142 Hom.: 9422 AF XY: 0.133 AC XY: 66896 AN XY: 502786

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.119

Gnomad4 ASJ exome AF: 0.182

Gnomad4 EAS exome AF: 0.0501

Gnomad4 SAS exome AF: 0.271

Gnomad4 FIN exome AF: 0.0785

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.132

GnomAD4 genome AF: 0.124 AC: 18811 AN: 152178 Hom.: 1257 Cov.: 31 AF XY: 0.124 AC XY: 9225 AN XY: 74402

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0392

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0999 Hom.: 297

Bravo AF: 0.126

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	This variant is associated with the following publications: (PMID: 17292373) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs561241; hg19: chr13-113760034;