rs10500359

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
LOC105371069	NR_197430.1	n.335-45387A>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.554 AC: 22983 AN: 41476

American (AMR) AF: 0.453 AC: 6914 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3466

East Asian (EAS) AF: 0.301 AC: 1557 AN: 5168

South Asian (SAS) AF: 0.153 AC: 741 AN: 4830

European-Finnish (FIN) AF: 0.294 AC: 3105 AN: 10578

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22964 AN: 67982

Other (OTH) AF: 0.401 AC: 846 AN: 2112

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10500359; hg19: chr16-8102613;