ENST00000750211.1:n.584-5621T>A

Variant names:

• chr9-119436925-A-T
• rs1331623
• ENST00000750211.1:n.584-5621T>A

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.584-5621T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,040 control chromosomes in the GnomAD database, including 29,680 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 0.60 (29680 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 5 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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 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.584-5621T>A		intron	N/A
	ENSG00000297691	ENST00000750214.1		n.194-5621T>A		intron	N/A
	ENSG00000297691	ENST00000750215.1		n.271-5621T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91298 AN: 151924 Hom.: 29667 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.601 AC: 91328 AN: 152040 Hom.: 29680 Cov.: 32 AF XY: 0.603 AC XY: 44802 AN XY: 74286

African (AFR) AF: 0.332 AC: 13775 AN: 41472

American (AMR) AF: 0.631 AC: 9622 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2347 AN: 3472

East Asian (EAS) AF: 0.546 AC: 2817 AN: 5164

South Asian (SAS) AF: 0.697 AC: 3354 AN: 4810

European-Finnish (FIN) AF: 0.747 AC: 7896 AN: 10576

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49277 AN: 67984

Other (OTH) AF: 0.609 AC: 1281 AN: 2102

Alfa AF: 0.651 Hom.: 4192

Bravo AF: 0.579

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1331623; hg19: chr9-122199203; COSMIC: COSV60399517;