chr9-134018215-C-T

Variant names:

• chr9-134018215-C-T
• rs482481
• ENST00000820247.1:n.146+6662G>A

Variant summary

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

The ENST00000820247.1(ENSG00000306694):​n.146+6662G>A variant causes a intron change. The variant allele was found at a frequency of 0.281 in 151,926 control chromosomes in the GnomAD database, including 6,693 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 0.28 (6693 hom., cov: 31)
• Consequence: ENSG00000306694 ENST00000820247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 5 publications found

Genes affected

ENSG00000306694 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820247.1. 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
	ENSG00000306694	ENST00000820247.1		n.146+6662G>A		intron	N/A
	ENSG00000306694	ENST00000820248.1		n.128+6666G>A		intron	N/A
	ENSG00000306694	ENST00000820249.1		n.427+3070G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42616 AN: 151808 Hom.: 6692 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.281 AC: 42649 AN: 151926 Hom.: 6693 Cov.: 31 AF XY: 0.293 AC XY: 21777 AN XY: 74246

African (AFR) AF: 0.176 AC: 7293 AN: 41450

American (AMR) AF: 0.301 AC: 4585 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3152 AN: 5152

South Asian (SAS) AF: 0.481 AC: 2318 AN: 4818

European-Finnish (FIN) AF: 0.395 AC: 4164 AN: 10542

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18996 AN: 67950

Other (OTH) AF: 0.286 AC: 602 AN: 2106

Alfa AF: 0.266 Hom.: 727

Bravo AF: 0.266

Asia WGS AF: 0.494 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.78

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: rs482481;

hg19: chr9-136883337;