rs1324467

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000290538 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647905.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290538	ENST00000647905.1		n.273-7150T>A		intron	N/A
	ENSG00000290538	ENST00000806593.1		n.57-7150T>A		intron	N/A
	ENSG00000290538	ENST00000806594.1		n.330-7150T>A		intron	N/A

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

African (AFR) AF: 0.0263 AC: 1091 AN: 41482

American (AMR) AF: 0.106 AC: 1624 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3466

East Asian (EAS) AF: 0.403 AC: 2083 AN: 5168

South Asian (SAS) AF: 0.169 AC: 815 AN: 4818

European-Finnish (FIN) AF: 0.131 AC: 1387 AN: 10568

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0754 AC: 5125 AN: 68000

Other (OTH) AF: 0.109 AC: 229 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		0.014

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1324467;

hg19: chr9-36005884;