rs4751264

Variant names:

• chr10-130740310-G-A
• rs4751264
• ENST00000834092.1:n.155-4431G>A

Variant summary

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

The ENST00000834092.1(ENSG00000308448):​n.155-4431G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,048 control chromosomes in the GnomAD database, including 827 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 0.091 (827 hom., cov: 32)
• Consequence: ENSG00000308448 ENST00000834092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

Genes affected

ENSG00000308448 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 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
ENSG00000308448	ENST00000834092.1	n.155-4431G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13825 AN: 151930 Hom.: 825 Cov.: 32

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0892

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0910 AC: 13840 AN: 152048 Hom.: 827 Cov.: 32 AF XY: 0.0908 AC XY: 6744 AN XY: 74298

African (AFR) AF: 0.0233 AC: 966 AN: 41508

American (AMR) AF: 0.122 AC: 1871 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3468

East Asian (EAS) AF: 0.0964 AC: 496 AN: 5144

South Asian (SAS) AF: 0.0872 AC: 419 AN: 4804

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10560

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7980 AN: 67978

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.108 Hom.: 917

Bravo AF: 0.0891

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4751264; hg19: chr10-132538574;