rs9450902

Variant names:

• chr6-88170505-C-G
• rs9450902
• ENST00000756364.1:n.129-41092C>G

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.129-41092C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,044 control chromosomes in the GnomAD database, including 2,682 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 0.16 (2682 hom., cov: 32)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.999
• Publications: 5 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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
ENSG00000298549	ENST00000756364.1	n.129-41092C>G		intron_variant	Intron 1 of 2
ENSG00000298549	ENST00000756365.1	n.571+236C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23820 AN: 151926 Hom.: 2677 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.157 AC: 23846 AN: 152044 Hom.: 2682 Cov.: 32 AF XY: 0.153 AC XY: 11373 AN XY: 74324

African (AFR) AF: 0.322 AC: 13329 AN: 41414

American (AMR) AF: 0.0997 AC: 1524 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3464

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5176

South Asian (SAS) AF: 0.0793 AC: 382 AN: 4816

European-Finnish (FIN) AF: 0.104 AC: 1102 AN: 10570

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6746 AN: 68004

Other (OTH) AF: 0.132 AC: 280 AN: 2114

Alfa AF: 0.130 Hom.: 227

Bravo AF: 0.163

Asia WGS AF: 0.0680 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.57
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs9450902; hg19: chr6-88880224;