rs10274759

Variant names:

• chr7-115274554-A-G
• rs10274759
• ENST00000753091.1:n.113-18907A>G

Variant summary

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

The ENST00000753091.1(ENSG00000298119):​n.113-18907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,282 control chromosomes in the GnomAD database, including 159 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 0.038 (159 hom., cov: 32)
• Consequence: ENSG00000298119 ENST00000753091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 5 publications found

Genes affected

ENSG00000298119 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0687 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
ENSG00000298119	ENST00000753091.1	n.113-18907A>G		intron_variant	Intron 1 of 4
ENSG00000298119	ENST00000753092.1	n.113-18907A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5846 AN: 152164 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.00621

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0230

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0385 AC: 5861 AN: 152282 Hom.: 159 Cov.: 32 AF XY: 0.0376 AC XY: 2799 AN XY: 74456

African (AFR) AF: 0.0697 AC: 2898 AN: 41566

American (AMR) AF: 0.0411 AC: 629 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0751 AC: 362 AN: 4822

European-Finnish (FIN) AF: 0.00621 AC: 66 AN: 10622

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0230 AC: 1561 AN: 68008

Other (OTH) AF: 0.0479 AC: 101 AN: 2110

Alfa AF: 0.0331 Hom.: 47

Bravo AF: 0.0418

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10274759; hg19: chr7-114914608;