15-77977130-A-G

Variant names:

• chr15-77977130-A-G
• rs12906542

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 0.154 in 152,028 control chromosomes in the GnomAD database, including 2,071 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 0.15 (2071 hom., cov: 33)
• Consequence: ADAMTS7P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 12 publications found

Genes affected

ADAMTS7P3 (HGNC:49409): (ADAMTS7 pseudogene 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.14).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566116.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS7P3	ENST00000566116.1	TSL:6	n.233-152A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23327 AN: 151910 Hom.: 2070 Cov.: 33

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.154 AC: 23340 AN: 152028 Hom.: 2071 Cov.: 33 AF XY: 0.154 AC XY: 11426 AN XY: 74308

African (AFR) AF: 0.0533 AC: 2207 AN: 41390

American (AMR) AF: 0.150 AC: 2291 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 425 AN: 3468

East Asian (EAS) AF: 0.152 AC: 785 AN: 5154

South Asian (SAS) AF: 0.157 AC: 756 AN: 4820

European-Finnish (FIN) AF: 0.204 AC: 2165 AN: 10602

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14147 AN: 67974

Other (OTH) AF: 0.142 AC: 301 AN: 2116

Alfa AF: 0.110 Hom.: 262

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.37
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs12906542; hg19: chr15-78269472;