rs4798812

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-9420506-G-A
• chr18-9420506-G-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759463.1. 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
	ENSG00000298966	ENST00000759463.1		n.271-315G>A		intron	N/A
	ENSG00000298966	ENST00000759464.1		n.232-315G>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs4798812;

hg19: chr18-9420504;