rs1490801

Variant names:

• chr5-67870680-A-G
• rs1490801
• ENST00000510621.5:n.57+31864T>C

Variant summary

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

The ENST00000510621.5(ENSG00000250421):​n.57+31864T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,920 control chromosomes in the GnomAD database, including 9,630 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 0.35 (9630 hom., cov: 32)
• Consequence: ENSG00000250421 ENST00000510621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 2 publications found

Genes affected

ENSG00000250421 (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 = 0.436 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
ENSG00000250421	ENST00000510621.5	n.57+31864T>C		intron_variant	Intron 1 of 3	4
ENSG00000249894	ENST00000514791.1	n.349+18922T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53111 AN: 151800 Hom.: 9619 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.350 AC: 53156 AN: 151920 Hom.: 9630 Cov.: 32 AF XY: 0.349 AC XY: 25945 AN XY: 74278

African (AFR) AF: 0.281 AC: 11632 AN: 41456

American (AMR) AF: 0.289 AC: 4411 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1310 AN: 5160

South Asian (SAS) AF: 0.451 AC: 2178 AN: 4824

European-Finnish (FIN) AF: 0.410 AC: 4337 AN: 10572

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27149 AN: 67878

Other (OTH) AF: 0.310 AC: 653 AN: 2108

Alfa AF: 0.388 Hom.: 6082

Bravo AF: 0.332

Asia WGS AF: 0.329 AC: 1146 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	5.7
DANN	Benign	0.78
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs1490801; hg19: chr5-67166508;