rs1941286

Positions:

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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000580366.1(ENSG00000263765):​n.27+5820A>G variant causes a intron, non coding transcript 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: ENST00000580366.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105372058	XR_001753390.2	n.424+5820A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000580366.1	n.27+5820A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000582239.1	n.393+5820A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.983

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.912

Alfa AF: 0.927 Hom.: 7947

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1941286; hg19: chr18-30420974;