rs7192208

Variant names:

• chr16-77295744-T-G
• rs7192208
• NM_199355.4:c.2802-617A>C

Variant summary

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

The NM_199355.4(ADAMTS18):​c.2802-617A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,210 control chromosomes in the GnomAD database, including 1,157 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 0.12 (1157 hom., cov: 32)
• Consequence: ADAMTS18 NM_199355.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495

Genes affected

ADAMTS18 (HGNC:17110): (ADAM metallopeptidase with thrombospondin type 1 motif 18) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. ADAMTS family members share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. The encoded preproprotein is proteolytically processed to generate the mature protein, which may regulate hemostatic balance and function as a tumor suppressor. Mutations in this gene may be associated with microcornea, myopic chorioretinal atrophy, and telecanthus (MMCAT) and cone-rod dystrophy in human patients. [provided by RefSeq, May 2016]

ENSG00000260922 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS18	NM_199355.4	c.2802-617A>C		intron_variant	Intron 18 of 22	ENST00000282849.10	NP_955387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS18	ENST00000282849.10	c.2802-617A>C		intron_variant	Intron 18 of 22	1	NM_199355.4	ENSP00000282849.5
ENSG00000260922	ENST00000648730.1	n.118-3146T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18025 AN: 152092 Hom.: 1151 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.119 AC: 18044 AN: 152210 Hom.: 1157 Cov.: 32 AF XY: 0.118 AC XY: 8746 AN XY: 74408

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.128

Alfa AF: 0.114 Hom.: 2059

Bravo AF: 0.123

Asia WGS AF: 0.202 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.55

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: rs7192208; hg19: chr16-77329641;