18-9420506-G-A

Variant names:

• chr18-9420506-G-A
• rs4798812
• ENST00000759463.1:n.271-315G>A

Variant summary

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

The ENST00000759463.1(ENSG00000298966):​n.271-315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,028 control chromosomes in the GnomAD database, including 7,011 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 0.30 (7011 hom., cov: 32)
• Consequence: ENSG00000298966 ENST00000759463.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 9 publications found

Genes affected

ENSG00000298966 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371980	XR_001753550.2	n.544-315G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298966	ENST00000759463.1	n.271-315G>A		intron_variant	Intron 1 of 1
ENSG00000298966	ENST00000759464.1	n.232-315G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44980 AN: 151910 Hom.: 6996 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.296 AC: 45031 AN: 152028 Hom.: 7011 Cov.: 32 AF XY: 0.296 AC XY: 21976 AN XY: 74326

African (AFR) AF: 0.238 AC: 9873 AN: 41444

American (AMR) AF: 0.439 AC: 6702 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1971 AN: 5156

South Asian (SAS) AF: 0.339 AC: 1633 AN: 4816

European-Finnish (FIN) AF: 0.218 AC: 2303 AN: 10568

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20284 AN: 67980

Other (OTH) AF: 0.315 AC: 665 AN: 2110

Alfa AF: 0.307 Hom.: 25016

Bravo AF: 0.315

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4798812; hg19: chr18-9420504;