rs10504833

Variant names:

• chr8-86839918-T-C
• rs10504833
• ENST00000723536.1:n.98-1641T>C

Variant summary

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

The ENST00000723536.1(ENSG00000294425):​n.98-1641T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 152,236 control chromosomes in the GnomAD database, including 1,227 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 0.072 (1227 hom., cov: 32)
• Consequence: ENSG00000294425 ENST00000723536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 0 publications found

Genes affected

ENSG00000294425 (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 = 0.234 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
ENSG00000294425	ENST00000723536.1	n.98-1641T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0717 AC: 10901 AN: 152120 Hom.: 1225 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00312

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0718 AC: 10934 AN: 152236 Hom.: 1227 Cov.: 32 AF XY: 0.0697 AC XY: 5193 AN XY: 74452

African (AFR) AF: 0.238 AC: 9891 AN: 41512

American (AMR) AF: 0.0314 AC: 480 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3468

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5182

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4826

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00312 AC: 212 AN: 68022

Other (OTH) AF: 0.0648 AC: 137 AN: 2114

Alfa AF: 0.0326 Hom.: 190

Bravo AF: 0.0823

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10504833; hg19: chr8-87852146;