rs9480303

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663591.1. 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
	ENSG00000287092	ENST00000663591.1		n.225-4418A>G		intron	N/A
	ENSG00000287092	ENST00000789128.1		n.309-4418A>G		intron	N/A
	ENSG00000287092	ENST00000789132.1		n.325-4418A>G		intron	N/A

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

African (AFR) AF: 0.540 AC: 22378 AN: 41452

American (AMR) AF: 0.328 AC: 5006 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2565 AN: 5168

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4816

European-Finnish (FIN) AF: 0.516 AC: 5442 AN: 10554

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28167 AN: 67890

Other (OTH) AF: 0.423 AC: 891 AN: 2106

Alfa AF: 0.443 Hom.: 3584

Bravo AF: 0.434

Asia WGS AF: 0.531 AC: 1842 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.54
DANN	Benign	0.58
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs9480303; hg19: chr6-156620306;