chr4-98522375-C-T

Variant names:

• chr4-98522375-C-T
• rs10516433
• NM_005723.4:c.82-14647G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005723.4(TSPAN5):​c.82-14647G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,076 control chromosomes in the GnomAD database, including 3,553 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 (3553 hom., cov: 33)
• Consequence: TSPAN5 NM_005723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 1 publications found

Genes affected

TSPAN5 (HGNC:17753): (tetraspanin 5) 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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005723.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN5	NM_005723.4	MANE Select	c.82-14647G>A		intron	N/A	NP_005714.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN5	ENST00000305798.8	TSL:1 MANE Select	c.82-14647G>A		intron	N/A	ENSP00000307701.3	P62079
	TSPAN5	ENST00000935829.1		c.82-14647G>A		intron	N/A	ENSP00000605888.1
	TSPAN5	ENST00000951778.1		c.82-14647G>A		intron	N/A	ENSP00000621837.1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32200 AN: 151958 Hom.: 3549 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.212 AC: 32222 AN: 152076 Hom.: 3553 Cov.: 33 AF XY: 0.206 AC XY: 15309 AN XY: 74336

African (AFR) AF: 0.231 AC: 9590 AN: 41482

American (AMR) AF: 0.176 AC: 2690 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 918 AN: 3472

East Asian (EAS) AF: 0.0945 AC: 489 AN: 5174

South Asian (SAS) AF: 0.246 AC: 1184 AN: 4810

European-Finnish (FIN) AF: 0.148 AC: 1570 AN: 10582

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14906 AN: 67970

Other (OTH) AF: 0.225 AC: 474 AN: 2106

Alfa AF: 0.216 Hom.: 469

Bravo AF: 0.211

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		-0.98
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: rs10516433; hg19: chr4-99443526;