rs1941286

Variant names:

• chr18-32841011-A-G
• rs1941286
• ENST00000580366.1:n.27+5820A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-32841011-A-G
• chr18-32841011-A-T

Variant summary

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

The ENST00000580366.1(ENSG00000263765):​n.27+5820A>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 152,178 control chromosomes in the GnomAD database, including 61,144 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 (61144 hom., cov: 31)
• Consequence: ENSG00000263765 ENST00000580366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404
• Publications: 1 publications found

Genes affected

ENSG00000263765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372058	XR_001753389.2	n.424+5820A>G		intron_variant	Intron 2 of 8
LOC105372058	XR_001753390.2	n.424+5820A>G		intron_variant	Intron 2 of 10
LOC105372058	XR_001753391.2	n.424+5820A>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263765	ENST00000580366.1	n.27+5820A>G		intron_variant	Intron 1 of 2	3
ENSG00000263765	ENST00000582239.1	n.393+5820A>G		intron_variant	Intron 2 of 3	5
ENSG00000263765	ENST00000798721.1	n.98+7488A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134153 AN: 152060 Hom.: 61125 Cov.: 31

Gnomad AFR AF: 0.627

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: 0.913

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

GnomAD4 genome AF: 0.882 AC: 134225 AN: 152178 Hom.: 61144 Cov.: 31 AF XY: 0.884 AC XY: 65795 AN XY: 74400

African (AFR) AF: 0.627 AC: 26013 AN: 41460

American (AMR) AF: 0.943 AC: 14427 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3421 AN: 3468

East Asian (EAS) AF: 0.991 AC: 5114 AN: 5162

South Asian (SAS) AF: 0.983 AC: 4740 AN: 4824

European-Finnish (FIN) AF: 0.968 AC: 10279 AN: 10620

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

European-Non Finnish (NFE) AF: 0.987 AC: 67134 AN: 68032

Other (OTH) AF: 0.912 AC: 1927 AN: 2112

Alfa AF: 0.916 Hom.: 8110

Asia WGS AF: 0.953 AC: 3314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1941286; hg19: chr18-30420974;