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:59091):

LOC105379066 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644559.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285190	ENST00000644559.1		n.720+5962G>A		intron	N/A
	ENSG00000285190	ENST00000797782.1		n.684+5962G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10065575;

hg19: chr5-86714840;

COSMIC: COSV63185556;