18-32836937-A-G

Variant names:

• chr18-32836937-A-G
• rs4799668
• ENST00000578782.2:n.429-972A>G

Variant summary

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

The ENST00000578782.2(ENSG00000263765):​n.429-972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,252 control chromosomes in the GnomAD database, including 61,184 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 0.88 (61184 hom., cov: 33)
• Consequence: ENSG00000263765 ENST00000578782.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 0 publications found

Genes affected

ENSG00000263765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578782.2. 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
	ENSG00000263765	ENST00000578782.2	TSL:3	n.429-972A>G		intron	N/A
	ENSG00000263765	ENST00000580366.1	TSL:3	n.27+1746A>G		intron	N/A
	ENSG00000263765	ENST00000582239.1	TSL:5	n.393+1746A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134235 AN: 152134 Hom.: 61165 Cov.: 33

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.882 AC: 134307 AN: 152252 Hom.: 61184 Cov.: 33 AF XY: 0.885 AC XY: 65846 AN XY: 74440

African (AFR) AF: 0.628 AC: 26035 AN: 41476

American (AMR) AF: 0.943 AC: 14441 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3423 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5124 AN: 5172

South Asian (SAS) AF: 0.983 AC: 4748 AN: 4832

European-Finnish (FIN) AF: 0.968 AC: 10284 AN: 10624

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67151 AN: 68046

Other (OTH) AF: 0.913 AC: 1931 AN: 2116

Alfa AF: 0.911 Hom.: 9521

Bravo AF: 0.869

Asia WGS AF: 0.953 AC: 3314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.74
DANN	Benign	0.66
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4799668; hg19: chr18-30416900;