5-87419023-G-A

Variant names:

• chr5-87419023-G-A
• rs10065575
• ENST00000644559.1:n.720+5962G>A

Variant summary

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

The ENST00000644559.1(ENSG00000285190):​n.720+5962G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,374 control chromosomes in the GnomAD database, including 17,404 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 0.48 (17404 hom., cov: 29)
• Consequence: ENSG00000285190 ENST00000644559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 4 publications found

Genes affected

ENSG00000285190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379066	XR_948542.2	n.77+5962G>A		intron_variant	Intron 1 of 3
LOC105379066	XR_948543.1	n.80+5962G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285190	ENST00000644559.1	n.720+5962G>A		intron_variant	Intron 1 of 4
ENSG00000285190	ENST00000797782.1	n.684+5962G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72073 AN: 151256 Hom.: 17382 Cov.: 29

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.477 AC: 72138 AN: 151374 Hom.: 17404 Cov.: 29 AF XY: 0.477 AC XY: 35274 AN XY: 73876

African (AFR) AF: 0.567 AC: 23418 AN: 41272

American (AMR) AF: 0.419 AC: 6370 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1598 AN: 3468

East Asian (EAS) AF: 0.508 AC: 2604 AN: 5130

South Asian (SAS) AF: 0.479 AC: 2298 AN: 4794

European-Finnish (FIN) AF: 0.454 AC: 4716 AN: 10386

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29517 AN: 67834

Other (OTH) AF: 0.495 AC: 1037 AN: 2096

Alfa AF: 0.447 Hom.: 30192

Bravo AF: 0.480

Asia WGS AF: 0.489 AC: 1699 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.84
DANN	Benign	0.36
PhyloP100		0.034

Splicing

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

Other links and lift over

dbSNP: rs10065575; hg19: chr5-86714840; COSMIC: COSV63185556;