rs1943919

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000263655 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263655	ENST00000581541.1	n.121+47619C>T		intron_variant	Intron 1 of 2	3

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

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.471

Alfa AF: 0.388 Hom.: 7092

Bravo AF: 0.518

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943919; hg19: chr18-71653657;