8-24186788-C-T

Variant names:

• chr8-24186788-C-T
• rs11777116
• ENST00000521681.3:n.322-3505G>A

Variant summary

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

The ENST00000521681.3(ADAM7-AS1):​n.322-3505G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0749 in 152,180 control chromosomes in the GnomAD database, including 484 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 0.075 (484 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000521681.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 7 publications found

Genes affected

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

LOC107986931 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521681.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM7-AS1	ENST00000521681.3	TSL:3	n.322-3505G>A		intron	N/A
	ADAM7-AS1	ENST00000773556.1		n.88-3505G>A		intron	N/A
	ADAM7-AS1	ENST00000773557.1		n.129-3505G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 11372 AN: 152062 Hom.: 480 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0749 AC: 11394 AN: 152180 Hom.: 484 Cov.: 32 AF XY: 0.0771 AC XY: 5738 AN XY: 74404

African (AFR) AF: 0.0538 AC: 2235 AN: 41520

American (AMR) AF: 0.0489 AC: 748 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3468

East Asian (EAS) AF: 0.151 AC: 782 AN: 5164

South Asian (SAS) AF: 0.143 AC: 689 AN: 4816

European-Finnish (FIN) AF: 0.0844 AC: 894 AN: 10590

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0787 AC: 5350 AN: 68012

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0720 Hom.: 510

Bravo AF: 0.0702

Asia WGS AF: 0.151 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.78
DANN	Benign	0.42
PhyloP100		0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11777116;

hg19: chr8-24044301;