rs1490800

chr5-67870719-T-Cchr5-67870719-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510621.5(ENSG00000250421):n.57+31825A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,006 control chromosomes in the GnomAD database, including 9,636 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 (9636 hom., cov: 32)
• Consequence: ENST00000510621.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000510621.5	n.57+31825A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000514791.1	n.349+18883A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53140 AN: 151888 Hom.: 9625 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.350 AC: 53184 AN: 152006 Hom.: 9636 Cov.: 32 AF XY: 0.349 AC XY: 25960 AN XY: 74328

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.309

Alfa AF: 0.369 Hom.: 11679

Bravo AF: 0.332

Asia WGS AF: 0.330 AC: 1146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1490800; hg19: chr5-67166547;