chr9-11402319-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286474 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375974	XR_001746618.1	n.73-45428C>A		intron_variant	Intron 1 of 5
LOC105375974	XR_007061893.1	n.73-45428C>A		intron_variant	Intron 1 of 4
LOC105375974	XR_929476.2	n.73-45428C>A		intron_variant	Intron 1 of 4
LOC105375974	XR_929477.2	n.73-45428C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286474	ENST00000657567.1	n.274-21073G>T		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.385

Alfa AF: 0.410 Hom.: 2785

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10809457; hg19: chr9-11402319;