rs9392465

Variant names:

• chr6-3162144-C-A
• rs9392465
• ENST00000842421.1:n.873+7606C>A

Variant summary

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

The ENST00000842421.1(ENSG00000309609):​n.873+7606C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,812 control chromosomes in the GnomAD database, including 26,195 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 0.57 (26195 hom., cov: 30)
• Consequence: ENSG00000309609 ENST00000842421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 23 publications found

Genes affected

ENSG00000309609 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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
ENSG00000309609	ENST00000842421.1	n.873+7606C>A		intron_variant	Intron 1 of 1
ENSG00000309609	ENST00000842422.1	n.939+7540C>A		intron_variant	Intron 1 of 1
ENSG00000309609	ENST00000842423.1	n.935+7544C>A		intron_variant	Intron 1 of 1
ENSG00000309609	ENST00000842424.1	n.156+7657C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86985 AN: 151694 Hom.: 26190 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.573 AC: 87023 AN: 151812 Hom.: 26195 Cov.: 30 AF XY: 0.571 AC XY: 42386 AN XY: 74186

African (AFR) AF: 0.409 AC: 16931 AN: 41350

American (AMR) AF: 0.519 AC: 7920 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2154 AN: 3464

East Asian (EAS) AF: 0.520 AC: 2677 AN: 5146

South Asian (SAS) AF: 0.411 AC: 1976 AN: 4808

European-Finnish (FIN) AF: 0.701 AC: 7386 AN: 10538

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 46022 AN: 67944

Other (OTH) AF: 0.603 AC: 1267 AN: 2102

Alfa AF: 0.638 Hom.: 134541

Bravo AF: 0.553

Asia WGS AF: 0.494 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs9392465; hg19: chr6-3162378;