rs2054096

chr15-58716644-T-Achr15-58716644-T-Cchr15-58716644-T-G

Variant summary

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

The NM_001110.4(ADAM10):c.206+933A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,062 control chromosomes in the GnomAD database, including 31,399 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 0.64 (31399 hom., cov: 32)
• Consequence: ADAM10 NM_001110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

ADAM10 (HGNC:188): (ADAM metallopeptidase domain 10) Members of the ADAM family are cell surface proteins with a unique structure possessing both potential adhesion and protease domains. This gene encodes and ADAM family member that cleaves many proteins including TNF-alpha and E-cadherin. Alternate splicing results in multiple transcript variants encoding different proteins that may undergo similar processing. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAM10	NM_001110.4	c.206+933A>T		intron_variant		ENST00000260408.8
ADAM10	NM_001320570.2	c.206+933A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAM10	ENST00000260408.8	c.206+933A>T		intron_variant		1	NM_001110.4	P1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96759 AN: 151944 Hom.: 31375 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.637 AC: 96830 AN: 152062 Hom.: 31399 Cov.: 32 AF XY: 0.633 AC XY: 47003 AN XY: 74290

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.679

Alfa AF: 0.672 Hom.: 4341

Bravo AF: 0.633

Asia WGS AF: 0.554 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	1.8
Dann	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs2054096; hg19: chr15-59008843;