rs1018466

Positions:

• chr14-36654045-A-C
• chr14-36654045-A-G

Variant summary

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

The XR_943758.3(LOC105370455):​n.1620T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,992 control chromosomes in the GnomAD database, including 18,723 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 0.49 (18723 hom., cov: 32)
• Consequence: LOC105370455 XR_943758.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

LOC105370455 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370455	XR_943758.3	n.1620T>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000555107.1	n.258+4499T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000634305.1	n.323-704A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74787 AN: 151874 Hom.: 18713 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.492 AC: 74838 AN: 151992 Hom.: 18723 Cov.: 32 AF XY: 0.490 AC XY: 36371 AN XY: 74300

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.501

Alfa AF: 0.520 Hom.: 41067

Bravo AF: 0.489

Asia WGS AF: 0.520 AC: 1811 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	0.035
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1018466; hg19: chr14-37123250;