rs10505250

Variant names:

• chr8-115267445-T-A
• rs10505250
• ENST00000748853.1:n.351+4311T>A

Variant summary

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

The ENST00000748853.1(ENSG00000297548):​n.351+4311T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 151,724 control chromosomes in the GnomAD database, including 321 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 0.045 (321 hom., cov: 32)
• Consequence: ENSG00000297548 ENST00000748853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 0 publications found

Genes affected

ENSG00000297548 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0996 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
ENSG00000297548	ENST00000748853.1	n.351+4311T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6848 AN: 151606 Hom.: 321 Cov.: 32

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.00406

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0381

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

GnomAD4 genome AF: 0.0452 AC: 6859 AN: 151724 Hom.: 321 Cov.: 32 AF XY: 0.0459 AC XY: 3404 AN XY: 74154

African (AFR) AF: 0.0994 AC: 4110 AN: 41344

American (AMR) AF: 0.0458 AC: 697 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3470

East Asian (EAS) AF: 0.0976 AC: 499 AN: 5114

South Asian (SAS) AF: 0.107 AC: 514 AN: 4790

European-Finnish (FIN) AF: 0.00406 AC: 43 AN: 10584

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 689 AN: 67902

Other (OTH) AF: 0.0391 AC: 82 AN: 2098

Alfa AF: 0.0298 Hom.: 17

Bravo AF: 0.0504

Asia WGS AF: 0.107 AC: 372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.74
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs10505250; hg19: chr8-116279674;