chr18-73986422-G-A

Variant names:

• chr18-73986422-G-A
• rs1943919
• ENST00000581541.1:n.121+47619C>T

Variant summary

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

The ENST00000581541.1(ENSG00000263655):​n.121+47619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,988 control chromosomes in the GnomAD database, including 21,398 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 0.50 (21398 hom., cov: 32)
• Consequence: ENSG00000263655 ENST00000581541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 4 publications found

Genes affected

ENSG00000263655 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581541.1. 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
	ENSG00000263655	ENST00000581541.1	TSL:3	n.121+47619C>T		intron	N/A
	ENSG00000287314	ENST00000753825.1		n.544-25088G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75452 AN: 151870 Hom.: 21342 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.497 AC: 75571 AN: 151988 Hom.: 21398 Cov.: 32 AF XY: 0.503 AC XY: 37363 AN XY: 74276

African (AFR) AF: 0.766 AC: 31769 AN: 41460

American (AMR) AF: 0.576 AC: 8798 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1601 AN: 5154

South Asian (SAS) AF: 0.505 AC: 2437 AN: 4822

European-Finnish (FIN) AF: 0.424 AC: 4475 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24049 AN: 67940

Other (OTH) AF: 0.471 AC: 996 AN: 2114

Alfa AF: 0.389 Hom.: 7872

Bravo AF: 0.518

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.17
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1943919; hg19: chr18-71653657;