rs7173049

Positions:

• chr15-73952269-A-G
• chr15-73952269-A-T

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 0.22 in 161,388 control chromosomes in the GnomAD database, including 4,095 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.22 (3860 hom., cov: 33)
  • Exomes 𝑓: 0.22 (235 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 15-73952269-A-G is Benign according to our data. Variant chr15-73952269-A-G is described in ClinVar as [Benign]. Clinvar id is 1266506.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 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: 0.220 AC: 33425 AN: 151978 Hom.: 3847 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.216 AC: 2003 AN: 9292 Hom.: 235 AF XY: 0.206 AC XY: 985 AN XY: 4772

Gnomad4 AFR exome AF: 0.226

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.314

Gnomad4 SAS exome AF: 0.412

Gnomad4 FIN exome AF: 0.185

Gnomad4 NFE exome AF: 0.206

Gnomad4 OTH exome AF: 0.238

GnomAD4 genome AF: 0.220 AC: 33470 AN: 152096 Hom.: 3860 Cov.: 33 AF XY: 0.223 AC XY: 16561 AN XY: 74344

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.246

Alfa AF: 0.211 Hom.: 4763

Bravo AF: 0.217

Asia WGS AF: 0.363 AC: 1263 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

Oct 16, 2019

This variant is associated with the following publications: (PMID: 30986821) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7173049; hg19: chr15-74244610;