rs10503756

Variant names:

• chr8-24617105-T-C
• rs10503756
• ENST00000519689.1:n.185-229114A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519689.1(ADAM7-AS1):​n.185-229114A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,302 control chromosomes in the GnomAD database, including 260 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 0.044 (260 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000519689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

ADAM7-AS1 (HGNC:56152): (ADAM7, ADAMDEC1 and ADAM28 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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
ADAM7-AS1	ENST00000519689.1	n.185-229114A>G		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6652 AN: 152184 Hom.: 258 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0438 AC: 6666 AN: 152302 Hom.: 260 Cov.: 32 AF XY: 0.0444 AC XY: 3310 AN XY: 74480

Gnomad4 AFR AF: 0.0851

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0267 Hom.: 15

Bravo AF: 0.0508

Asia WGS AF: 0.111 AC: 384 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503756; hg19: chr8-24474618;