rs2866016

Variant names:

• chr4-98583084-G-A
• rs2866016
• NM_005723.4:c.81+75062C>T

Variant summary

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

The NM_005723.4(TSPAN5):​c.81+75062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,098 control chromosomes in the GnomAD database, including 47,449 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 0.78 (47449 hom., cov: 32)
• Consequence: TSPAN5 NM_005723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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.81+75062C>T		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.81+75062C>T		intron	N/A	ENSP00000307701.3	P62079
	TSPAN5	ENST00000935829.1		c.81+75062C>T		intron	N/A	ENSP00000605888.1
	TSPAN5	ENST00000951778.1		c.81+75062C>T		intron	N/A	ENSP00000621837.1

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119118 AN: 151980 Hom.: 47395 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.784 AC: 119237 AN: 152098 Hom.: 47449 Cov.: 32 AF XY: 0.786 AC XY: 58443 AN XY: 74332

African (AFR) AF: 0.924 AC: 38369 AN: 41530

American (AMR) AF: 0.784 AC: 11983 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2490 AN: 3468

East Asian (EAS) AF: 0.693 AC: 3559 AN: 5136

South Asian (SAS) AF: 0.855 AC: 4116 AN: 4812

European-Finnish (FIN) AF: 0.755 AC: 7985 AN: 10570

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48182 AN: 67990

Other (OTH) AF: 0.754 AC: 1587 AN: 2106

Alfa AF: 0.736 Hom.: 36524

Bravo AF: 0.789

Asia WGS AF: 0.805 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.34
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: rs2866016; hg19: chr4-99504235;