rs9480303

Variant names:

• chr6-156299172-T-C
• rs9480303
• ENST00000663591.1:n.225-4418A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663591.1(ENSG00000287092):​n.225-4418A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,940 control chromosomes in the GnomAD database, including 15,800 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 0.45 (15800 hom., cov: 32)
• Consequence: ENSG00000287092 ENST00000663591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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
ENSG00000287092	ENST00000663591.1	n.225-4418A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68069 AN: 151822 Hom.: 15780 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.448 AC: 68140 AN: 151940 Hom.: 15800 Cov.: 32 AF XY: 0.452 AC XY: 33565 AN XY: 74256

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.423

Alfa AF: 0.441 Hom.: 3468

Bravo AF: 0.434

Asia WGS AF: 0.531 AC: 1842 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.54
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9480303; hg19: chr6-156620306;