rs7172432

Variant names:

• chr15-62104190-A-G
• rs7172432

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.505 in 151,966 control chromosomes in the GnomAD database, including 20,417 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 0.51 (20417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 110 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.675 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: 0.505 AC: 76675 AN: 151848 Hom.: 20358 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.505 AC: 76804 AN: 151966 Hom.: 20417 Cov.: 32 AF XY: 0.507 AC XY: 37635 AN XY: 74278

African (AFR) AF: 0.682 AC: 28268 AN: 41442

American (AMR) AF: 0.477 AC: 7281 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1919 AN: 5162

South Asian (SAS) AF: 0.383 AC: 1847 AN: 4820

European-Finnish (FIN) AF: 0.555 AC: 5861 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28816 AN: 67948

Other (OTH) AF: 0.494 AC: 1040 AN: 2104

Alfa AF: 0.443 Hom.: 53207

Bravo AF: 0.507

Asia WGS AF: 0.446 AC: 1550 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	4.4
DANN	Benign	0.48
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7172432; hg19: chr15-62396389;