rs1324467

Variant names:

• chr9-36005887-T-A
• rs1324467
• ENST00000647905.1:n.273-7150T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647905.1(ENSG00000290538):​n.273-7150T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,096 control chromosomes in the GnomAD database, including 943 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 0.084 (943 hom., cov: 32)
• Consequence: ENSG00000290538 ENST00000647905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

ENSG00000290538 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290538	ENST00000647905.1	n.273-7150T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0837 AC: 12727 AN: 151978 Hom.: 935 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0838 AC: 12746 AN: 152096 Hom.: 943 Cov.: 32 AF XY: 0.0883 AC XY: 6568 AN XY: 74344

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0698

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0754

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0776 Hom.: 70

Bravo AF: 0.0801

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	15
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324467; hg19: chr9-36005884;