ENST00000562876.2:n.500C>T

Variant names:

• chr16-1275970-G-A
• rs1962736
• ENST00000562876.2:n.500C>T

Variant summary

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

The ENST00000562876.2(ENSG00000261564):​n.500C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,846 control chromosomes in the GnomAD database, including 20,162 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 0.50 (20162 hom., cov: 32)
• Consequence: ENSG00000261564 ENST00000562876.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 8 publications found

Genes affected

ENSG00000261564 (HGNC:):

TPSP1 (HGNC:14182):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPSP1		n.1275970G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261564	ENST00000562876.2	n.500C>T		non_coding_transcript_exon_variant	Exon 3 of 5	6

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76390 AN: 151728 Hom.: 20145 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.503 AC: 76446 AN: 151846 Hom.: 20162 Cov.: 32 AF XY: 0.518 AC XY: 38407 AN XY: 74206

African (AFR) AF: 0.447 AC: 18506 AN: 41370

American (AMR) AF: 0.578 AC: 8829 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1511 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4746 AN: 5152

South Asian (SAS) AF: 0.753 AC: 3621 AN: 4808

European-Finnish (FIN) AF: 0.577 AC: 6092 AN: 10560

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31674 AN: 67906

Other (OTH) AF: 0.475 AC: 999 AN: 2102

Alfa AF: 0.476 Hom.: 21762

Bravo AF: 0.498

Asia WGS AF: 0.764 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1962736; hg19: chr16-1325971;