chr18-5942644-G-A

Variant names:

• chr18-5942644-G-A
• rs564021
• ENST00000659442.1:n.342+46558G>A

Variant summary

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

The ENST00000659442.1(ENSG00000266846):​n.342+46558G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,178 control chromosomes in the GnomAD database, including 45,294 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 0.77 (45294 hom., cov: 32)
• Consequence: ENSG00000266846 ENST00000659442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 2 publications found

Genes affected

ENSG00000266846 (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 = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC121725015	NR_172504.1	n.361-42365G>A		intron_variant	Intron 1 of 2
LOC121725015	NR_172505.1	n.361-42359G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266846	ENST00000659442.1	n.342+46558G>A		intron_variant	Intron 1 of 7
ENSG00000264449	ENST00000659662.1	n.212-42359G>A		intron_variant	Intron 1 of 2
ENSG00000264449	ENST00000664630.1	n.332-42365G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116479 AN: 152060 Hom.: 45252 Cov.: 32

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.766 AC: 116582 AN: 152178 Hom.: 45294 Cov.: 32 AF XY: 0.767 AC XY: 57076 AN XY: 74382

African (AFR) AF: 0.898 AC: 37311 AN: 41560

American (AMR) AF: 0.689 AC: 10532 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2320 AN: 3472

East Asian (EAS) AF: 0.814 AC: 4201 AN: 5158

South Asian (SAS) AF: 0.761 AC: 3672 AN: 4824

European-Finnish (FIN) AF: 0.737 AC: 7800 AN: 10580

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48371 AN: 67986

Other (OTH) AF: 0.722 AC: 1528 AN: 2116

Alfa AF: 0.719 Hom.: 139180

Bravo AF: 0.766

Asia WGS AF: 0.762 AC: 2651 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	0.21
DANN	Benign	0.71
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs564021; hg19: chr18-5942643;