7-120824495-C-T

Position:

• chr7-120824495-C-T

Variant summary

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

The NM_012338.4(TSPAN12):​c.286-8692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,778 control chromosomes in the GnomAD database, including 14,183 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 0.40 (14183 hom., cov: 31)
• Consequence: TSPAN12 NM_012338.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

Genes affected

TSPAN12 (HGNC:21641): (tetraspanin 12) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSPAN12	NM_012338.4	c.286-8692G>A		intron_variant		ENST00000222747.8
TSPAN12	XM_005250239.4	c.286-8692G>A		intron_variant
TSPAN12	XM_047420095.1	c.286-8692G>A		intron_variant
TSPAN12	XM_047420096.1	c.286-13925G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPAN12	ENST00000222747.8	c.286-8692G>A		intron_variant		1	NM_012338.4	P1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59868 AN: 151660 Hom.: 14139 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.395 AC: 59986 AN: 151778 Hom.: 14183 Cov.: 31 AF XY: 0.398 AC XY: 29493 AN XY: 74176

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.352

Alfa AF: 0.205 Hom.: 466

Bravo AF: 0.408

Asia WGS AF: 0.360 AC: 1253 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.38

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: rs6953454; hg19: chr7-120464549;