rs6478915

Variant names:

• chr9-129762171-G-A
• rs6478915
• ENST00000730689.1:n.382-847C>T

Variant summary

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

The ENST00000730689.1(ENSG00000295529):​n.382-847C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,016 control chromosomes in the GnomAD database, including 46,308 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 0.78 (46308 hom., cov: 30)
• Consequence: ENSG00000295529 ENST00000730689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 1 publications found

Genes affected

ENSG00000295529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730689.1. 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
	ENSG00000295529	ENST00000730689.1		n.382-847C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118165 AN: 151898 Hom.: 46269 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.778 AC: 118260 AN: 152016 Hom.: 46308 Cov.: 30 AF XY: 0.780 AC XY: 57966 AN XY: 74296

African (AFR) AF: 0.798 AC: 33097 AN: 41460

American (AMR) AF: 0.824 AC: 12585 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5126 AN: 5160

South Asian (SAS) AF: 0.796 AC: 3840 AN: 4822

European-Finnish (FIN) AF: 0.729 AC: 7706 AN: 10570

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50957 AN: 67944

Other (OTH) AF: 0.773 AC: 1635 AN: 2114

Alfa AF: 0.762 Hom.: 9212

Bravo AF: 0.788

Asia WGS AF: 0.883 AC: 3068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.13
DANN	Benign	0.58
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6478915; hg19: chr9-132524450;