rs9294320

Variant names:

• chr6-84955316-G-A
• rs9294320
• ENST00000804923.1:n.68+21292C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-84955316-G-A
• chr6-84955316-G-T

Variant summary

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

The ENST00000804923.1(ENSG00000304604):​n.68+21292C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 151,992 control chromosomes in the GnomAD database, including 1,579 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 0.094 (1579 hom., cov: 32)
• Consequence: ENSG00000304604 ENST00000804923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 0 publications found

Genes affected

ENSG00000304604 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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
ENSG00000304604	ENST00000804923.1	n.68+21292C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0937 AC: 14238 AN: 151874 Hom.: 1578 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0158

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0937 AC: 14248 AN: 151992 Hom.: 1579 Cov.: 32 AF XY: 0.0925 AC XY: 6874 AN XY: 74300

African (AFR) AF: 0.267 AC: 11074 AN: 41422

American (AMR) AF: 0.0402 AC: 614 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0154 AC: 74 AN: 4820

European-Finnish (FIN) AF: 0.0365 AC: 385 AN: 10554

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0278 AC: 1889 AN: 67982

Other (OTH) AF: 0.0651 AC: 137 AN: 2106

Alfa AF: 0.0981 Hom.: 888

Bravo AF: 0.101

Asia WGS AF: 0.0160 AC: 55 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs9294320; hg19: chr6-85665034;