rs7173512

Variant names:

• chr15-78557572-C-T
• rs7173512

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 0.697 in 151,228 control chromosomes in the GnomAD database, including 37,259 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 0.70 (37259 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.697 AC: 105345 AN: 151110 Hom.: 37202 Cov.: 29

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.697 AC: 105464 AN: 151228 Hom.: 37259 Cov.: 29 AF XY: 0.701 AC XY: 51816 AN XY: 73878

African (AFR) AF: 0.768 AC: 31749 AN: 41356

American (AMR) AF: 0.779 AC: 11684 AN: 15004

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2286 AN: 3460

East Asian (EAS) AF: 0.823 AC: 4118 AN: 5004

South Asian (SAS) AF: 0.748 AC: 3584 AN: 4794

European-Finnish (FIN) AF: 0.662 AC: 6945 AN: 10490

Middle Eastern (MID) AF: 0.783 AC: 227 AN: 290

European-Non Finnish (NFE) AF: 0.632 AC: 42848 AN: 67822

Other (OTH) AF: 0.711 AC: 1498 AN: 2108

Alfa AF: 0.657 Hom.: 4165

Bravo AF: 0.708

Asia WGS AF: 0.770 AC: 2672 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.40
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7173512; hg19: chr15-78849914;