rs7172832

chr15-70393164-T-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 0.447 in 151,892 control chromosomes in the GnomAD database, including 15,611 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 0.45 (15611 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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 (AMR) allele frequency at 95% confidence interval = 0.484 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: 0.446 AC: 67762 AN: 151774 Hom.: 15587 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.447 AC: 67836 AN: 151892 Hom.: 15611 Cov.: 31 AF XY: 0.444 AC XY: 32974 AN XY: 74236

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.470

Alfa AF: 0.470 Hom.: 2663

Bravo AF: 0.452

Asia WGS AF: 0.335 AC: 1162 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	1.3
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7172832; hg19: chr15-70685503;