9-11402319-G-T

Variant names:

• chr9-11402319-G-T
• rs10809457
• ENST00000657567.1:n.274-21073G>T

Variant summary

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

The ENST00000657567.1(ENSG00000286474):​n.274-21073G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,664 control chromosomes in the GnomAD database, including 10,202 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 0.35 (10202 hom., cov: 32)
• Consequence: ENSG00000286474 ENST00000657567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 1 publications found

Genes affected

ENSG00000286474 (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 (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657567.1. 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
	ENSG00000286474	ENST00000657567.1		n.274-21073G>T		intron	N/A
	ENSG00000230365	ENST00000799517.1		n.239-45428C>A		intron	N/A
	ENSG00000286474	ENST00000799774.1		n.207-21073G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53440 AN: 151546 Hom.: 10197 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.353 AC: 53470 AN: 151664 Hom.: 10202 Cov.: 32 AF XY: 0.349 AC XY: 25824 AN XY: 74082

African (AFR) AF: 0.251 AC: 10409 AN: 41412

American (AMR) AF: 0.292 AC: 4450 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3466

East Asian (EAS) AF: 0.115 AC: 590 AN: 5150

South Asian (SAS) AF: 0.233 AC: 1120 AN: 4812

European-Finnish (FIN) AF: 0.431 AC: 4527 AN: 10496

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29331 AN: 67790

Other (OTH) AF: 0.385 AC: 814 AN: 2112

Alfa AF: 0.402 Hom.: 17570

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.1
DANN	Benign	0.47
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs10809457; hg19: chr9-11402319;