9-119502298-A-G

Variant names:

• chr9-119502298-A-G
• rs10491523
• ENST00000565320.1:n.183+6741A>G

Variant summary

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

The ENST00000565320.1(ENSG00000260970):​n.183+6741A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0222 in 152,296 control chromosomes in the GnomAD database, including 112 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 0.022 (112 hom., cov: 33)
• Consequence: ENSG00000260970 ENST00000565320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 2 publications found

Genes affected

ENSG00000260970 (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 = 0.0697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376250	XR_930304.2	n.188+21597T>C		intron_variant	Intron 1 of 2
LOC105376250	XR_930305.2	n.188+21597T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260970	ENST00000565320.1	n.183+6741A>G		intron_variant	Intron 1 of 2	3
ENSG00000297691	ENST00000750211.1	n.584-70994T>C		intron_variant	Intron 6 of 7
ENSG00000297691	ENST00000750214.1	n.193+21597T>C		intron_variant	Intron 1 of 2
ENSG00000297691	ENST00000750215.1	n.158-20108T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0221 AC: 3370 AN: 152178 Hom.: 109 Cov.: 33

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00219

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0222 AC: 3385 AN: 152296 Hom.: 112 Cov.: 33 AF XY: 0.0208 AC XY: 1548 AN XY: 74464

African (AFR) AF: 0.0718 AC: 2984 AN: 41548

American (AMR) AF: 0.0111 AC: 170 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4824

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00219 AC: 149 AN: 68030

Other (OTH) AF: 0.0203 AC: 43 AN: 2114

Alfa AF: 0.0129 Hom.: 4

Bravo AF: 0.0248

Asia WGS AF: 0.00635 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.059
DANN	Benign	0.50
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10491523; hg19: chr9-122264576;