9-119496299-C-T

Variant names:

• chr9-119496299-C-T
• rs10984561
• ENST00000565320.1:n.183+742C>T

Variant summary

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

The ENST00000565320.1(ENSG00000260970):​n.183+742C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0607 in 152,096 control chromosomes in the GnomAD database, including 302 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 0.061 (302 hom., cov: 32)
• Consequence: ENSG00000260970 ENST00000565320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376250	XR_930304.2	n.188+27596G>A		intron_variant	Intron 1 of 2
LOC105376250	XR_930305.2	n.188+27596G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260970	ENST00000565320.1	n.183+742C>T		intron_variant	Intron 1 of 2	3
ENSG00000297691	ENST00000750211.1	n.584-64995G>A		intron_variant	Intron 6 of 7
ENSG00000297691	ENST00000750214.1	n.193+27596G>A		intron_variant	Intron 1 of 2
ENSG00000297691	ENST00000750215.1	n.158-14109G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9224 AN: 151978 Hom.: 302 Cov.: 32

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.0420

Gnomad FIN AF: 0.0492

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0531

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0607 AC: 9230 AN: 152096 Hom.: 302 Cov.: 32 AF XY: 0.0600 AC XY: 4461 AN XY: 74348

African (AFR) AF: 0.0849 AC: 3521 AN: 41454

American (AMR) AF: 0.0359 AC: 549 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.0863 AC: 447 AN: 5182

South Asian (SAS) AF: 0.0422 AC: 203 AN: 4808

European-Finnish (FIN) AF: 0.0492 AC: 521 AN: 10594

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0531 AC: 3608 AN: 67988

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0540 Hom.: 729

Bravo AF: 0.0606

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10984561; hg19: chr9-122258577;