ENST00000565320.1:n.183+742C>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565320.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260970	ENST00000565320.1	TSL:3	n.183+742C>T		intron	N/A
	ENSG00000297691	ENST00000750211.1		n.584-64995G>A		intron	N/A
	ENSG00000297691	ENST00000750214.1		n.193+27596G>A		intron	N/A

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 v4.9

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;