rs10500359

Variant names:

• chr16-8052611-T-A
• rs10500359
• ENST00000567103.2:n.302-45387A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567103.2(ENSG00000260289):​n.302-45387A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,078 control chromosomes in the GnomAD database, including 13,091 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 0.40 (13091 hom., cov: 33)
• Consequence: ENSG00000260289 ENST00000567103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260289	ENST00000567103.2	n.302-45387A>T		intron_variant	Intron 1 of 3	5
ENSG00000260289	ENST00000654046.1	n.335-45387A>T		intron_variant	Intron 1 of 3
ENSG00000260289	ENST00000670665.1	n.335-45387A>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60423 AN: 151960 Hom.: 13055 Cov.: 33

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.398 AC: 60519 AN: 152078 Hom.: 13091 Cov.: 33 AF XY: 0.394 AC XY: 29263 AN XY: 74348

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.401

Alfa AF: 0.371 Hom.: 1398

Bravo AF: 0.424

Asia WGS AF: 0.228 AC: 793 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500359; hg19: chr16-8102613;