rs1124941

Variant names:

• chr18-77187841-C-A
• rs1124941
• ENST00000584843.1:n.209+2544C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-77187841-C-A
• chr18-77187841-C-T

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.209+2544C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 150,976 control chromosomes in the GnomAD database, including 16,526 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 0.47 (16526 hom., cov: 30)
• Consequence: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 6 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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
ENSG00000265844	ENST00000584843.1	n.209+2544C>A		intron_variant	Intron 2 of 4	4
ENSG00000265844	ENST00000843890.1	n.415-623C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70107 AN: 150858 Hom.: 16487 Cov.: 30

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.465 AC: 70205 AN: 150976 Hom.: 16526 Cov.: 30 AF XY: 0.472 AC XY: 34741 AN XY: 73662

African (AFR) AF: 0.530 AC: 21834 AN: 41180

American (AMR) AF: 0.518 AC: 7822 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3464

East Asian (EAS) AF: 0.448 AC: 2278 AN: 5086

South Asian (SAS) AF: 0.438 AC: 2086 AN: 4764

European-Finnish (FIN) AF: 0.503 AC: 5202 AN: 10346

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27899 AN: 67748

Other (OTH) AF: 0.450 AC: 940 AN: 2088

Alfa AF: 0.425 Hom.: 44710

Bravo AF: 0.464

Asia WGS AF: 0.485 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.24
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1124941; hg19: chr18-74899797;