rs1362781

Positions:

• chr18-55771805-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654829.1(ENSG00000267284):​n.157-13094G>A 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 0.228 in 151,642 control chromosomes in the GnomAD database, including 4,399 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 0.23 (4399 hom., cov: 31)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372130	XR_007066382.1	n.329-13094G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654829.1	n.157-13094G>A		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.455-902G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.218-13094G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34571 AN: 151524 Hom.: 4392 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.228 AC: 34614 AN: 151642 Hom.: 4399 Cov.: 31 AF XY: 0.230 AC XY: 17071 AN XY: 74138

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.225

Alfa AF: 0.248 Hom.: 591

Bravo AF: 0.230

Asia WGS AF: 0.199 AC: 687 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362781; hg19: chr18-53439036;