NM_001288973.2:c.88+2402A>G

Variant names:

• chr10-126385656-T-C
• rs7081193
• NM_001288973.2:c.88+2402A>G

Variant summary

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

The NM_001288973.2(ADAM12):​c.88+2402A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,008 control chromosomes in the GnomAD database, including 536 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 0.082 (536 hom., cov: 32)
• Consequence: ADAM12 NM_001288973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 2 publications found

Genes affected

ADAM12 (HGNC:190): (ADAM metallopeptidase domain 12) This gene encodes a member of a family of proteins that are structurally related to snake venom disintegrins and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. Expression of this gene has been used as a maternal serum marker for pre-natal development. Alternative splicing results in multiple transcript variants encoding different isoforms. Shorter isoforms are secreted, while longer isoforms are membrane-bound form. [provided by RefSeq, Jan 2014]

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 (NFE) allele frequency at 95% confidence interval = 0.0857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAM12	NM_001288973.2	c.88+2402A>G		intron_variant	Intron 1 of 22	ENST00000448723.2	NP_001275902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAM12	ENST00000448723.2	c.88+2402A>G		intron_variant	Intron 1 of 22	5	NM_001288973.2	ENSP00000391268.2
ADAM12	ENST00000368679.8	c.88+2402A>G		intron_variant	Intron 1 of 22	1		ENSP00000357668.4
ADAM12	ENST00000368676.8	c.88+2402A>G		intron_variant	Intron 1 of 18	1		ENSP00000357665.4

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12445 AN: 151890 Hom.: 537 Cov.: 32

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0847

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.0643

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.0819 AC: 12448 AN: 152008 Hom.: 536 Cov.: 32 AF XY: 0.0807 AC XY: 5997 AN XY: 74294

African (AFR) AF: 0.0757 AC: 3138 AN: 41456

American (AMR) AF: 0.0846 AC: 1293 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.0652 AC: 337 AN: 5170

South Asian (SAS) AF: 0.0640 AC: 308 AN: 4814

European-Finnish (FIN) AF: 0.0675 AC: 712 AN: 10546

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0876 AC: 5950 AN: 67952

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.0890 Hom.: 1033

Bravo AF: 0.0855

Asia WGS AF: 0.0560 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.75
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7081193; hg19: chr10-128074225;