ENST00000510621.5:n.57+31825A>G

Variant names:

• chr5-67870719-T-C
• rs1490800
• ENST00000510621.5:n.57+31825A>G

Variant summary

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

The ENST00000510621.5(ENSG00000250421):​n.57+31825A>G 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 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: ENSG00000250421 ENST00000510621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 4 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=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250421	ENST00000510621.5	n.57+31825A>G		intron_variant	Intron 1 of 3	4
ENSG00000249894	ENST00000514791.1	n.349+18883A>G		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.281 AC: 11639 AN: 41480

American (AMR) AF: 0.289 AC: 4415 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1314 AN: 5166

South Asian (SAS) AF: 0.451 AC: 2176 AN: 4828

European-Finnish (FIN) AF: 0.410 AC: 4333 AN: 10572

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

European-Non Finnish (NFE) AF: 0.400 AC: 27168 AN: 67924

Other (OTH) AF: 0.309 AC: 652 AN: 2108

Alfa AF: 0.362 Hom.: 18802

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1490800; hg19: chr5-67166547;