rs9480154

Variant names:

• chr6-150289479-G-A
• rs9480154
• ENST00000806617.1:n.269-5301G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-150289479-G-A
• chr6-150289479-G-T

Variant summary

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

The ENST00000806617.1(ENSG00000304854):​n.269-5301G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,108 control chromosomes in the GnomAD database, including 662 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 0.082 (662 hom., cov: 32)
• Consequence: ENSG00000304854 ENST00000806617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 2 publications found

Genes affected

ENSG00000304854 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806617.1. 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
	ENSG00000304854	ENST00000806617.1		n.269-5301G>A		intron	N/A
	ENSG00000304854	ENST00000806618.1		n.165-5301G>A		intron	N/A
	ENSG00000304854	ENST00000806619.1		n.140-5301G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12434 AN: 151992 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0817 AC: 12428 AN: 152108 Hom.: 662 Cov.: 32 AF XY: 0.0852 AC XY: 6334 AN XY: 74362

African (AFR) AF: 0.0825 AC: 3422 AN: 41470

American (AMR) AF: 0.0697 AC: 1065 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5162

South Asian (SAS) AF: 0.169 AC: 812 AN: 4810

European-Finnish (FIN) AF: 0.0659 AC: 699 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0650 AC: 4420 AN: 67988

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.0723 Hom.: 770

Bravo AF: 0.0803

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.31
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs9480154; hg19: chr6-150610615; COSMIC: COSV69430212;