18-38483901-T-C

Variant names:

• chr18-38483901-T-C
• rs1365463
• ENST00000809738.1:n.203+6180A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000809738.1(ENSG00000305237):​n.203+6180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 151,808 control chromosomes in the GnomAD database, including 51,732 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 0.82 (51732 hom., cov: 29)
• Consequence: ENSG00000305237 ENST00000809738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 2 publications found

Genes affected

ENSG00000305237 (HGNC:58979):

LOC105372074 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809738.1. 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
	ENSG00000305237	ENST00000809738.1		n.203+6180A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124146 AN: 151690 Hom.: 51708 Cov.: 29

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.818 AC: 124228 AN: 151808 Hom.: 51732 Cov.: 29 AF XY: 0.817 AC XY: 60639 AN XY: 74178

African (AFR) AF: 0.662 AC: 27386 AN: 41342

American (AMR) AF: 0.850 AC: 12956 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2971 AN: 3470

East Asian (EAS) AF: 0.577 AC: 2953 AN: 5120

South Asian (SAS) AF: 0.790 AC: 3810 AN: 4820

European-Finnish (FIN) AF: 0.906 AC: 9562 AN: 10554

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61819 AN: 67950

Other (OTH) AF: 0.833 AC: 1759 AN: 2112

Alfa AF: 0.876 Hom.: 218459

Bravo AF: 0.805

Asia WGS AF: 0.691 AC: 2405 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	19
DANN	Benign	0.81
PhyloP100		1.4

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: rs1365463;

hg19: chr18-36063865;