rs7902355

Positions:

• chr10-80489352-C-T

Variant summary

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

The NM_030927.4(TSPAN14):​c.81+38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,306,214 control chromosomes in the GnomAD database, including 38,797 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 0.21 (3573 hom., cov: 33)
  • Exomes 𝑓: 0.24 (35224 hom.)
• Consequence: TSPAN14 NM_030927.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

TSPAN14 (HGNC:23303): (tetraspanin 14) Enables enzyme binding activity. Involved in positive regulation of Notch signaling pathway; protein localization to plasma membrane; and protein maturation. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSPAN14	NM_030927.4	c.81+38C>T		intron_variant		ENST00000429989.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPAN14	ENST00000429989.8	c.81+38C>T		intron_variant		1	NM_030927.4	P1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31705 AN: 152062 Hom.: 3564 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.236

GnomAD3 exomes AF: 0.234 AC: 37328 AN: 159394 Hom.: 4939 AF XY: 0.241 AC XY: 20176 AN XY: 83736

Gnomad AFR exome AF: 0.141

Gnomad AMR exome AF: 0.242

Gnomad ASJ exome AF: 0.281

Gnomad EAS exome AF: 0.0214

Gnomad SAS exome AF: 0.329

Gnomad FIN exome AF: 0.245

Gnomad NFE exome AF: 0.241

Gnomad OTH exome AF: 0.243

GnomAD4 exome AF: 0.237 AC: 273179 AN: 1154034 Hom.: 35224 Cov.: 15 AF XY: 0.240 AC XY: 139486 AN XY: 581324

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.245

Gnomad4 ASJ exome AF: 0.283

Gnomad4 EAS exome AF: 0.0167

Gnomad4 SAS exome AF: 0.329

Gnomad4 FIN exome AF: 0.251

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.230

GnomAD4 genome AF: 0.209 AC: 31732 AN: 152180 Hom.: 3573 Cov.: 33 AF XY: 0.212 AC XY: 15774 AN XY: 74410

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.239

Alfa AF: 0.240 Hom.: 2518

Bravo AF: 0.203

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7902355; hg19: chr10-82249108;