rs9650409

Variant names:

• chr8-24383191-G-A
• rs9650409
• ENST00000518988.5:n.355+3970C>T

Variant summary

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

The ENST00000518988.5(ADAM7-AS1):​n.355+3970C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,904 control chromosomes in the GnomAD database, including 11,284 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 0.37 (11284 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000518988.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAM7-AS1	NR_125808.1	n.501+3970C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAM7-AS1	ENST00000518988.5	n.355+3970C>T		intron_variant	Intron 1 of 3	2
ADAM7-AS1	ENST00000519689.1	n.606+3970C>T		intron_variant	Intron 4 of 4	4
ADAM7-AS1	ENST00000523578.5	n.501+3970C>T		intron_variant	Intron 3 of 3	4
ADAM7-AS1	ENST00000523700.5	n.164+3970C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56817 AN: 151786 Hom.: 11277 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.374 AC: 56850 AN: 151904 Hom.: 11284 Cov.: 32 AF XY: 0.375 AC XY: 27813 AN XY: 74220

African (AFR) AF: 0.250 AC: 10376 AN: 41432

American (AMR) AF: 0.438 AC: 6666 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3464

East Asian (EAS) AF: 0.187 AC: 968 AN: 5164

South Asian (SAS) AF: 0.405 AC: 1953 AN: 4824

European-Finnish (FIN) AF: 0.431 AC: 4545 AN: 10546

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.434 AC: 29489 AN: 67932

Other (OTH) AF: 0.369 AC: 777 AN: 2108

Alfa AF: 0.414 Hom.: 57596

Bravo AF: 0.367

Asia WGS AF: 0.324 AC: 1127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.15
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs9650409; hg19: chr8-24240704;