rs10075974

Variant names:

• chr5-92444950-A-G
• rs10075974
• ENST00000507217.5:n.528+29266A>G

Variant summary

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

The ENST00000507217.5(ENSG00000250049):​n.528+29266A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 151,810 control chromosomes in the GnomAD database, including 282 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 0.057 (282 hom., cov: 31)
• Consequence: ENSG00000250049 ENST00000507217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 1 publications found

Genes affected

ENSG00000250049 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379080	XR_001742806.2	n.5737+29266A>G		intron_variant	Intron 4 of 4
LOC105379080	XR_007058867.1	n.5590+29266A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250049	ENST00000507217.5	n.528+29266A>G		intron_variant	Intron 3 of 3	4
ENSG00000249776	ENST00000512210.5	n.406-34589T>C		intron_variant	Intron 3 of 3	3
ENSG00000249776	ENST00000513779.1	n.253-12661T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8716 AN: 151692 Hom.: 284 Cov.: 31

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.0947

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0574 AC: 8710 AN: 151810 Hom.: 282 Cov.: 31 AF XY: 0.0570 AC XY: 4231 AN XY: 74170

African (AFR) AF: 0.0386 AC: 1601 AN: 41484

American (AMR) AF: 0.0506 AC: 769 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5166

South Asian (SAS) AF: 0.0718 AC: 346 AN: 4822

European-Finnish (FIN) AF: 0.0761 AC: 805 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4539 AN: 67794

Other (OTH) AF: 0.0712 AC: 150 AN: 2108

Alfa AF: 0.0667 Hom.: 189

Bravo AF: 0.0542

Asia WGS AF: 0.0440 AC: 154 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10075974; hg19: chr5-91780657;