rs951299

Variant names:

• chr4-98676725-A-C
• rs951299
• ENST00000802021.1:n.128+17703A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-98676725-A-C
• chr4-98676725-A-T

Variant summary

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

The ENST00000802021.1(TSPAN5-DT):​n.128+17703A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,042 control chromosomes in the GnomAD database, including 18,358 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 0.46 (18358 hom., cov: 32)
• Consequence: TSPAN5-DT ENST00000802021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 5 publications found

Genes affected

TSPAN5-DT (HGNC:55389): (TSPAN5 divergent transcript)

LOC112267901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267901	XR_939016.3	n.315-1250A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPAN5-DT	ENST00000802021.1	n.128+17703A>C		intron_variant	Intron 1 of 2
TSPAN5-DT	ENST00000802027.1	n.279-1250A>C		intron_variant	Intron 2 of 2
TSPAN5-DT	ENST00000802028.1	n.214-1250A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69317 AN: 151922 Hom.: 18314 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.457 AC: 69429 AN: 152042 Hom.: 18358 Cov.: 32 AF XY: 0.458 AC XY: 34008 AN XY: 74324

African (AFR) AF: 0.734 AC: 30432 AN: 41462

American (AMR) AF: 0.452 AC: 6907 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1654 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1103 AN: 5168

South Asian (SAS) AF: 0.452 AC: 2179 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3858 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.321 AC: 21815 AN: 67970

Other (OTH) AF: 0.465 AC: 982 AN: 2114

Alfa AF: 0.305 Hom.: 1162

Bravo AF: 0.472

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0060
DANN	Benign	0.57
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs951299; hg19: chr4-99597876;