9-119796312-T-A

Variant names:

• chr9-119796312-T-A
• rs11792644
• ENST00000750211.1:n.368+9363A>T

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.368+9363A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0534 in 152,182 control chromosomes in the GnomAD database, including 296 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 0.053 (296 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 2 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
	ENSG00000297691	ENST00000750211.1		n.368+9363A>T		intron	N/A
	ENSG00000297691	ENST00000750212.1		n.385-23622A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8120 AN: 152064 Hom.: 296 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0448

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0534 AC: 8121 AN: 152182 Hom.: 296 Cov.: 32 AF XY: 0.0520 AC XY: 3866 AN XY: 74386

African (AFR) AF: 0.0149 AC: 617 AN: 41538

American (AMR) AF: 0.0419 AC: 641 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4822

European-Finnish (FIN) AF: 0.0672 AC: 712 AN: 10588

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0827 AC: 5620 AN: 67990

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

Alfa AF: 0.0620 Hom.: 47

Bravo AF: 0.0500

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs11792644; hg19: chr9-122558590;