rs10491524

Variant names:

• chr9-119494976-T-C
• rs10491524
• ENST00000750211.1:n.584-63672A>G

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.584-63672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,104 control chromosomes in the GnomAD database, including 33,037 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 0.65 (33037 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 7 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
	ENSG00000297691	ENST00000750211.1		n.584-63672A>G		intron	N/A
	ENSG00000297691	ENST00000750214.1		n.193+28919A>G		intron	N/A
	ENSG00000297691	ENST00000750215.1		n.158-12786A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98378 AN: 151986 Hom.: 33012 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.0982

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.647 AC: 98440 AN: 152104 Hom.: 33037 Cov.: 32 AF XY: 0.640 AC XY: 47578 AN XY: 74350

African (AFR) AF: 0.654 AC: 27131 AN: 41478

American (AMR) AF: 0.565 AC: 8636 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3472

East Asian (EAS) AF: 0.0986 AC: 511 AN: 5180

South Asian (SAS) AF: 0.486 AC: 2335 AN: 4806

European-Finnish (FIN) AF: 0.714 AC: 7547 AN: 10576

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47695 AN: 67996

Other (OTH) AF: 0.639 AC: 1346 AN: 2106

Alfa AF: 0.677 Hom.: 44956

Bravo AF: 0.637

Asia WGS AF: 0.292 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.9
DANN	Benign	0.74
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10491524; hg19: chr9-122257254;