rs9321490

Variant names:

• chr6-135173737-T-C
• rs9321490
• ENST00000774085.1:n.-60A>G

Variant summary

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

The ENST00000774085.1(ENSG00000300795):​n.-60A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,032 control chromosomes in the GnomAD database, including 5,215 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 0.26 (5215 hom., cov: 31)
• Consequence: ENSG00000300795 ENST00000774085.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 21 publications found

Genes affected

ENSG00000300795 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774085.1. 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
	ENSG00000300795	ENST00000774085.1		n.-60A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39055 AN: 151914 Hom.: 5203 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.257 AC: 39098 AN: 152032 Hom.: 5215 Cov.: 31 AF XY: 0.261 AC XY: 19425 AN XY: 74320

African (AFR) AF: 0.262 AC: 10841 AN: 41436

American (AMR) AF: 0.287 AC: 4385 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1917 AN: 5162

South Asian (SAS) AF: 0.347 AC: 1672 AN: 4816

European-Finnish (FIN) AF: 0.294 AC: 3103 AN: 10562

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15630 AN: 67986

Other (OTH) AF: 0.272 AC: 575 AN: 2116

Alfa AF: 0.243 Hom.: 7164

Bravo AF: 0.259

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.11
DANN	Benign	0.77
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9321490;

hg19: chr6-135494875;