rs7173943

chr15-99552246-G-C

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 0.648 in 152,150 control chromosomes in the GnomAD database, including 33,601 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 0.65 (33585 hom., cov: 30)
  • Exomes 𝑓: 0.37 (16 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 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: 0.649 AC: 98436 AN: 151774 Hom.: 33537 Cov.: 30

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.372 AC: 96 AN: 258 Hom.: 16 AF XY: 0.372 AC XY: 61 AN XY: 164

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.417

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.365

Gnomad4 OTH exome AF: 0.389

GnomAD4 genome AF: 0.649 AC: 98538 AN: 151892 Hom.: 33585 Cov.: 30 AF XY: 0.649 AC XY: 48122 AN XY: 74184

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.640

Alfa AF: 0.594 Hom.: 3517

Bravo AF: 0.657

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7173943; hg19: chr15-100092451;