rs10516862

Variant names:

• chr4-90076020-G-T
• rs10516862
• ENST00000740240.1:n.115-24098C>A

Variant summary

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

The ENST00000740240.1(ENSG00000296542):​n.115-24098C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,996 control chromosomes in the GnomAD database, including 8,088 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 0.31 (8088 hom., cov: 32)
• Consequence: ENSG00000296542 ENST00000740240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 4 publications found

Genes affected

ENSG00000296542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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
ENSG00000296542	ENST00000740240.1	n.115-24098C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46734 AN: 151878 Hom.: 8090 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.307 AC: 46731 AN: 151996 Hom.: 8088 Cov.: 32 AF XY: 0.308 AC XY: 22883 AN XY: 74294

African (AFR) AF: 0.161 AC: 6686 AN: 41470

American (AMR) AF: 0.276 AC: 4211 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5172

South Asian (SAS) AF: 0.288 AC: 1389 AN: 4816

European-Finnish (FIN) AF: 0.425 AC: 4489 AN: 10556

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27021 AN: 67918

Other (OTH) AF: 0.277 AC: 585 AN: 2114

Alfa AF: 0.359 Hom.: 1296

Bravo AF: 0.291

Asia WGS AF: 0.244 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.37
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs10516862; hg19: chr4-90997171;