rs25812

Variant names:

• chr5-103037888-T-C
• rs25812
• ENST00000826594.1:n.104-4913A>G

Variant summary

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

The ENST00000826594.1(ENSG00000307497):​n.104-4913A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 152,306 control chromosomes in the GnomAD database, including 46 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 0.020 (46 hom., cov: 32)
• Consequence: ENSG00000307497 ENST00000826594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 0 publications found

Genes affected

ENSG00000307497 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0574 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
ENSG00000307497	ENST00000826594.1	n.104-4913A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2988 AN: 152188 Hom.: 46 Cov.: 32

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.00650

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0197 AC: 2993 AN: 152306 Hom.: 46 Cov.: 32 AF XY: 0.0211 AC XY: 1569 AN XY: 74490

African (AFR) AF: 0.0191 AC: 792 AN: 41566

American (AMR) AF: 0.0437 AC: 669 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3470

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5184

South Asian (SAS) AF: 0.0632 AC: 305 AN: 4824

European-Finnish (FIN) AF: 0.00650 AC: 69 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 956 AN: 68030

Other (OTH) AF: 0.0232 AC: 49 AN: 2110

Alfa AF: 0.0140 Hom.: 29

Bravo AF: 0.0191

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.024
DANN	Benign	0.30
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs25812; hg19: chr5-102373592;