rs9959454

Variant names:

• chr18-79010820-A-G
• rs9959454
• ENST00000836199.1:n.558-9044T>C

Variant summary

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

The ENST00000836199.1(ENSG00000308736):​n.558-9044T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,136 control chromosomes in the GnomAD database, including 5,392 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 (5392 hom., cov: 33)
• Consequence: ENSG00000308736 ENST00000836199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 11 publications found

Genes affected

ENSG00000308736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836199.1. 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
	ENSG00000308736	ENST00000836199.1		n.558-9044T>C		intron	N/A
	ENSG00000308736	ENST00000836200.1		n.451-9044T>C		intron	N/A
	ENSG00000308736	ENST00000836201.1		n.532-8374T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39989 AN: 152018 Hom.: 5385 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.263 AC: 40010 AN: 152136 Hom.: 5392 Cov.: 33 AF XY: 0.266 AC XY: 19787 AN XY: 74366

African (AFR) AF: 0.237 AC: 9849 AN: 41506

American (AMR) AF: 0.252 AC: 3859 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2067 AN: 5172

South Asian (SAS) AF: 0.334 AC: 1612 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2850 AN: 10560

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17946 AN: 68000

Other (OTH) AF: 0.265 AC: 561 AN: 2114

Alfa AF: 0.262 Hom.: 2254

Bravo AF: 0.260

Asia WGS AF: 0.349 AC: 1210 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.50
PhyloP100		-0.34

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: rs9959454;

hg19: chr18-76770820;