rs4798765

Variant names:

• chr18-9083405-T-C
• rs4798765
• ENST00000827765.1:n.264+10363A>G

Variant summary

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

The ENST00000827765.1(ENSG00000288939):​n.264+10363A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,082 control chromosomes in the GnomAD database, including 32,217 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 0.65 (32217 hom., cov: 32)
• Consequence: ENSG00000288939 ENST00000827765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 3 publications found

Genes affected

ENSG00000288939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827765.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288939	ENST00000827765.1		n.264+10363A>G		intron	N/A
	ENSG00000288939	ENST00000827767.1		n.242-2941A>G		intron	N/A
	ENSG00000307687	ENST00000827902.1		n.167-451T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98707 AN: 151964 Hom.: 32205 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.649 AC: 98765 AN: 152082 Hom.: 32217 Cov.: 32 AF XY: 0.656 AC XY: 48753 AN XY: 74330

African (AFR) AF: 0.595 AC: 24688 AN: 41466

American (AMR) AF: 0.635 AC: 9690 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2211 AN: 3468

East Asian (EAS) AF: 0.671 AC: 3472 AN: 5172

South Asian (SAS) AF: 0.752 AC: 3622 AN: 4814

European-Finnish (FIN) AF: 0.745 AC: 7865 AN: 10564

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45018 AN: 68012

Other (OTH) AF: 0.648 AC: 1369 AN: 2112

Alfa AF: 0.658 Hom.: 42415

Bravo AF: 0.637

Asia WGS AF: 0.666 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.48
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs4798765; hg19: chr18-9083403;