rs13175726

Variant names:

• chr5-97051329-A-G
• rs13175726
• ENST00000788211.1:n.191+1795A>G

Variant summary

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

The ENST00000788211.1(ENSG00000302623):​n.191+1795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,030 control chromosomes in the GnomAD database, including 7,366 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 0.31 (7366 hom., cov: 32)
• Consequence: ENSG00000302623 ENST00000788211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 5 publications found

Genes affected

ENSG00000302623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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
ENSG00000302623	ENST00000788211.1	n.191+1795A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46367 AN: 151912 Hom.: 7350 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.305 AC: 46434 AN: 152030 Hom.: 7366 Cov.: 32 AF XY: 0.302 AC XY: 22453 AN XY: 74358

African (AFR) AF: 0.396 AC: 16404 AN: 41424

American (AMR) AF: 0.250 AC: 3812 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1290 AN: 5178

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4826

European-Finnish (FIN) AF: 0.246 AC: 2603 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19193 AN: 67970

Other (OTH) AF: 0.298 AC: 628 AN: 2106

Alfa AF: 0.291 Hom.: 25620

Bravo AF: 0.307

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs13175726; hg19: chr5-96387033; COSMIC: COSV60168164;