rs10516579

Variant names:

• chr4-111762367-T-C
• rs10516579
• ENST00000751011.1:n.125+40273A>G

Variant summary

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

The ENST00000751011.1(ENSG00000297804):​n.125+40273A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0167 in 152,294 control chromosomes in the GnomAD database, including 87 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 0.017 (87 hom., cov: 32)
• Consequence: ENSG00000297804 ENST00000751011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• Publications: 2 publications found

Genes affected

ENSG00000297804 (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 (EAS) allele frequency at 95% confidence interval = 0.117 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
ENSG00000297804	ENST00000751011.1	n.125+40273A>G		intron_variant	Intron 1 of 3
ENSG00000297804	ENST00000751012.1	n.89+40273A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0167 AC: 2537 AN: 152176 Hom.: 84 Cov.: 32

Gnomad AFR AF: 0.00277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00809

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0167 AC: 2547 AN: 152294 Hom.: 87 Cov.: 32 AF XY: 0.0182 AC XY: 1355 AN XY: 74466

African (AFR) AF: 0.00276 AC: 115 AN: 41592

American (AMR) AF: 0.0579 AC: 885 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.125 AC: 645 AN: 5174

South Asian (SAS) AF: 0.0101 AC: 49 AN: 4830

European-Finnish (FIN) AF: 0.0225 AC: 239 AN: 10620

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00807 AC: 549 AN: 68010

Other (OTH) AF: 0.0166 AC: 35 AN: 2110

Alfa AF: 0.0106 Hom.: 33

Bravo AF: 0.0203

Asia WGS AF: 0.0500 AC: 173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.42
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs10516579; hg19: chr4-112683523;