rs10792032

Variant names:

• chr11-69217135-G-A
• rs10792032
• ENST00000779509.1:n.138+20953G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000779509.1(ENSG00000301530):​n.138+20953G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,260 control chromosomes in the GnomAD database, including 18,911 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 0.49 (18911 hom., cov: 30)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 7 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779509.1. 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
	ENSG00000301530	ENST00000779509.1		n.138+20953G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.489 AC: 73894 AN: 151142 Hom.: 18876 Cov.: 30

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0695

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.489 AC: 73978 AN: 151260 Hom.: 18911 Cov.: 30 AF XY: 0.483 AC XY: 35648 AN XY: 73862

African (AFR) AF: 0.562 AC: 23127 AN: 41146

American (AMR) AF: 0.383 AC: 5822 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2283 AN: 3462

East Asian (EAS) AF: 0.0687 AC: 353 AN: 5142

South Asian (SAS) AF: 0.327 AC: 1566 AN: 4792

European-Finnish (FIN) AF: 0.471 AC: 4930 AN: 10456

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34249 AN: 67736

Other (OTH) AF: 0.515 AC: 1084 AN: 2106

Alfa AF: 0.504 Hom.: 3421

Bravo AF: 0.488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10792032; hg19: chr11-68984602;