rs7902355

Variant names:

• chr10-80489352-C-T
• rs7902355
• NM_030927.4:c.81+38C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030927.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN14	NM_030927.4	MANE Select	c.81+38C>T		intron	N/A	NP_112189.2
	TSPAN14	NM_001351266.2		c.81+38C>T		intron	N/A	NP_001338195.1
	TSPAN14	NM_001351267.4		c.81+38C>T		intron	N/A	NP_001338196.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN14	ENST00000429989.8	TSL:1 MANE Select	c.81+38C>T		intron	N/A	ENSP00000396270.2
	TSPAN14	ENST00000372164.7	TSL:1	c.81+38C>T		intron	N/A	ENSP00000361237.3
	TSPAN14	ENST00000714439.1		c.81+38C>T		intron	N/A	ENSP00000519708.1

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

GnomAD2 exomes AF: 0.234 AC: 37328 AN: 159394 AF XY: 0.241

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 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

African (AFR) AF: 0.130 AC: 3475 AN: 26814

American (AMR) AF: 0.245 AC: 8684 AN: 35466

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 6698 AN: 23652

East Asian (EAS) AF: 0.0167 AC: 586 AN: 35146

South Asian (SAS) AF: 0.329 AC: 24416 AN: 74224

European-Finnish (FIN) AF: 0.251 AC: 12350 AN: 49126

Middle Eastern (MID) AF: 0.270 AC: 1342 AN: 4978

European-Non Finnish (NFE) AF: 0.239 AC: 204113 AN: 854538

Other (OTH) AF: 0.230 AC: 11515 AN: 50090

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

African (AFR) AF: 0.134 AC: 5575 AN: 41530

American (AMR) AF: 0.264 AC: 4037 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3468

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5182

South Asian (SAS) AF: 0.314 AC: 1512 AN: 4822

European-Finnish (FIN) AF: 0.253 AC: 2673 AN: 10572

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16077 AN: 67994

Other (OTH) AF: 0.239 AC: 506 AN: 2114

Alfa AF: 0.241 Hom.: 2751

Bravo AF: 0.203

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.43
PhyloP100		0.058
PromoterAI		0.0065	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7902355; hg19: chr10-82249108; COSMIC: COSV107401181;