rs10098562

Variant names:

• chr8-108940833-G-A
• rs10098562
• ENST00000522244.1:n.265-22187C>T

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.265-22187C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,028 control chromosomes in the GnomAD database, including 2,056 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 0.11 (2056 hom., cov: 31)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 2 publications found

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927413	NR_188033.1	n.134+7942C>T		intron_variant	Intron 1 of 3
LOC101927413	NR_188034.1	n.134+7942C>T		intron_variant	Intron 1 of 3
LOC101927413	NR_188035.1	n.134+7942C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253796	ENST00000522244.1	n.265-22187C>T		intron_variant	Intron 3 of 4	3
ENSG00000253796	ENST00000656015.4	n.145+7942C>T		intron_variant	Intron 1 of 3
ENSG00000253796	ENST00000702172.1	n.134+7942C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17245 AN: 151910 Hom.: 2049 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0536

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.114 AC: 17285 AN: 152028 Hom.: 2056 Cov.: 31 AF XY: 0.115 AC XY: 8535 AN XY: 74312

African (AFR) AF: 0.300 AC: 12429 AN: 41422

American (AMR) AF: 0.0613 AC: 937 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0210 AC: 73 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.141 AC: 680 AN: 4822

European-Finnish (FIN) AF: 0.0536 AC: 566 AN: 10558

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0346 AC: 2349 AN: 67980

Other (OTH) AF: 0.0999 AC: 211 AN: 2112

Alfa AF: 0.0858 Hom.: 216

Bravo AF: 0.119

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.6
DANN	Benign	0.77
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10098562; hg19: chr8-109953062;