rs7168365

Positions:

• chr15-53513628-C-A
• chr15-53513628-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.375 in 151,852 control chromosomes in the GnomAD database, including 11,147 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.37 (11147 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53513628C>A		intergenic_region
LOC105370826	XR_007064643.1	n.167-376C>A		intron_variant
LOC105370826	XR_007064644.1	n.315-376C>A		intron_variant
LOC105370826	XR_007064645.1	n.167-376C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56829 AN: 151734 Hom.: 11134 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.375 AC: 56884 AN: 151852 Hom.: 11147 Cov.: 32 AF XY: 0.377 AC XY: 27966 AN XY: 74218

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.400

Alfa AF: 0.404 Hom.: 15179

Bravo AF: 0.382

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7168365; hg19: chr15-53805825;