rs4529792

Variant names:

• chr10-64182569-C-A
• rs4529792
• ENST00000654191.1:n.597-118947C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-64182569-C-A
• chr10-64182569-C-G
• chr10-64182569-C-T

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.597-118947C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 152,124 control chromosomes in the GnomAD database, including 40,442 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 0.67 (40442 hom., cov: 33)
• Consequence: ENSG00000228566 ENST00000654191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902439	XR_007062160.1	n.576-118947C>A		intron_variant	Intron 3 of 5
LOC124902439	XR_007062161.1	n.578-118947C>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228566	ENST00000654191.1	n.597-118947C>A		intron_variant	Intron 3 of 5
ENSG00000228566	ENST00000660795.1	n.346-118947C>A		intron_variant	Intron 3 of 6
ENSG00000228566	ENST00000764124.1	n.329+91239C>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101328 AN: 152006 Hom.: 40442 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.666 AC: 101331 AN: 152124 Hom.: 40442 Cov.: 33 AF XY: 0.672 AC XY: 49986 AN XY: 74382

African (AFR) AF: 0.191 AC: 7925 AN: 41440

American (AMR) AF: 0.761 AC: 11639 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3064 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4371 AN: 5174

South Asian (SAS) AF: 0.798 AC: 3846 AN: 4818

European-Finnish (FIN) AF: 0.844 AC: 8959 AN: 10614

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58968 AN: 67998

Other (OTH) AF: 0.704 AC: 1489 AN: 2114

Alfa AF: 0.819 Hom.: 23016

Bravo AF: 0.638

Asia WGS AF: 0.783 AC: 2706 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.32
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4529792; hg19: chr10-65942330;