rs1018836

chr8-90558134-A-Gchr8-90558134-A-T

Variant summary

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

The ENST00000665012.1(ENSG00000254180):n.142-3468T>C 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 0.466 in 152,062 control chromosomes in the GnomAD database, including 17,588 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 0.47 (17588 hom., cov: 32)
• Consequence: ENST00000665012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

Genes affected

(HGNC:):

LINC00534 (HGNC:43643): (long intergenic non-protein coding RNA 534)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901975	XR_007061002.1	n.43-3468T>C		intron_variant, non_coding_transcript_variant
LOC124901975	XR_007061003.1	n.113-3468T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665012.1	n.142-3468T>C		intron_variant, non_coding_transcript_variant
LINC00534	ENST00000667296.1	n.456+103611A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70774 AN: 151944 Hom.: 17544 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.466 AC: 70879 AN: 152062 Hom.: 17588 Cov.: 32 AF XY: 0.468 AC XY: 34759 AN XY: 74342

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.464

Alfa AF: 0.392 Hom.: 5691

Bravo AF: 0.493

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.85
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1018836; hg19: chr8-91570362;