rs10491074

Variant names:

• chr10-64058802-A-G
• rs10491074
• ENST00000654191.1:n.517-1324A>G

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.517-1324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 152,226 control chromosomes in the GnomAD database, including 940 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 0.076 (940 hom., cov: 32)
• Consequence: ENSG00000228566 ENST00000654191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 1 publications found

Genes affected

ENSG00000228566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654191.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228566	ENST00000654191.1		n.517-1324A>G		intron	N/A
	ENSG00000228566	ENST00000660795.1		n.266-1324A>G		intron	N/A
	ENSG00000228566	ENST00000764129.1		n.211-1324A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11546 AN: 152108 Hom.: 936 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0761 AC: 11583 AN: 152226 Hom.: 940 Cov.: 32 AF XY: 0.0739 AC XY: 5502 AN XY: 74428

African (AFR) AF: 0.202 AC: 8402 AN: 41516

American (AMR) AF: 0.0650 AC: 995 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3470

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5182

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4818

European-Finnish (FIN) AF: 0.00528 AC: 56 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0216 AC: 1467 AN: 68006

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0566 Hom.: 103

Bravo AF: 0.0883

Asia WGS AF: 0.0470 AC: 162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.9
DANN	Benign	0.79
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10491074; hg19: chr10-65818562;