chr8-24617105-T-C

Position:

• chr8-24617105-T-C

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAM7-AS1	ENST00000519689.1	n.185-229114A>G		intron_variant, non_coding_transcript_variant		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;