rs10074959

Variant names:

• chr5-104872312-G-A
• rs10074959
• ENST00000503650.1:n.328+14546C>T

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.328+14546C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,868 control chromosomes in the GnomAD database, including 7,466 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 0.30 (7466 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 2 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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
ENSG00000251574	ENST00000503650.1	n.328+14546C>T		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000524336.5	n.190+14546C>T		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000807455.1	n.133+14546C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44806 AN: 151750 Hom.: 7459 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.295 AC: 44840 AN: 151868 Hom.: 7466 Cov.: 32 AF XY: 0.291 AC XY: 21581 AN XY: 74206

African (AFR) AF: 0.453 AC: 18734 AN: 41392

American (AMR) AF: 0.215 AC: 3275 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1371 AN: 5120

South Asian (SAS) AF: 0.150 AC: 721 AN: 4820

European-Finnish (FIN) AF: 0.252 AC: 2659 AN: 10568

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16349 AN: 67946

Other (OTH) AF: 0.282 AC: 594 AN: 2106

Alfa AF: 0.258 Hom.: 21792

Bravo AF: 0.301

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10074959; hg19: chr5-104208013;