9-104264531-C-T

Variant names:

• chr9-104264531-C-T
• rs1450679
• ENST00000745188.1:n.605-60518G>A

Variant summary

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

The ENST00000745188.1(ENSG00000297079):​n.605-60518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,126 control chromosomes in the GnomAD database, including 57,404 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 0.87 (57404 hom., cov: 31)
• Consequence: ENSG00000297079 ENST00000745188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967
• Publications: 8 publications found

Genes affected

ENSG00000297079 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745188.1. 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
	ENSG00000297079	ENST00000745188.1		n.605-60518G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131634 AN: 152008 Hom.: 57363 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.866 AC: 131733 AN: 152126 Hom.: 57404 Cov.: 31 AF XY: 0.864 AC XY: 64218 AN XY: 74358

African (AFR) AF: 0.940 AC: 39052 AN: 41528

American (AMR) AF: 0.770 AC: 11749 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3097 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4912 AN: 5172

South Asian (SAS) AF: 0.803 AC: 3874 AN: 4822

European-Finnish (FIN) AF: 0.862 AC: 9119 AN: 10582

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57053 AN: 67982

Other (OTH) AF: 0.875 AC: 1849 AN: 2112

Alfa AF: 0.847 Hom.: 86902

Bravo AF: 0.866

Asia WGS AF: 0.858 AC: 2986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	11
DANN	Benign	0.41
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs1450679; hg19: chr9-107026812;