15-58621262-CAAAAAAAA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001110.4(ADAM10):c.1511+201_1511+208del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (201 hom., cov: 20)
• Consequence: ADAM10 NM_001110.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.63

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 -10 ACMG points.

• BP6: Variant 15-58621262-CAAAAAAAA-C is Benign according to our data. Variant chr15-58621262-CAAAAAAAA-C is described in ClinVar as [Benign]. Clinvar id is 1238913.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAM10	NM_001110.4	c.1511+201_1511+208del		intron_variant		ENST00000260408.8
ADAM10	NM_001320570.2	c.1418+201_1418+208del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAM10	ENST00000260408.8	c.1511+201_1511+208del		intron_variant		1	NM_001110.4	P1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 4015 AN: 25168 Hom.: 201 Cov.: 20

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00909

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.00738

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.160 AC: 4021 AN: 25182 Hom.: 201 Cov.: 20 AF XY: 0.159 AC XY: 1855 AN XY: 11642

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.0749

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00909

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00738

Gnomad4 OTH AF: 0.134

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs749439192; hg19: chr15-58913461;