rs7172832

Variant names:

• chr15-70393164-T-C
• rs7172832

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;