18-56025735-C-A

Variant names:

• chr18-56025735-C-A
• rs2646965
• ENST00000666716.1:n.2714C>A

Variant summary

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

The ENST00000666716.1(LINC01905):​n.2714C>A 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 0.535 in 151,868 control chromosomes in the GnomAD database, including 22,705 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 0.54 (22705 hom., cov: 32)
• Consequence: LINC01905 ENST00000666716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 0 publications found

Genes affected

LINC01905 (HGNC:52724): (long intergenic non-protein coding RNA 1905)

LINC03092 (HGNC:56721): (long intergenic non-protein coding RNA 3092)

LINC01539 (HGNC:51307): (long intergenic non-protein coding RNA 1539)

LINC03069 (HGNC:56641): (long intergenic non-protein coding RNA 3069)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666716.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03069	NR_148972.1		n.2212-340G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01905	ENST00000666716.1		n.2714C>A		non_coding_transcript_exon	Exon 2 of 2
	LINC01539	ENST00000382897.2	TSL:2	n.2212-340G>T		intron	N/A
	LINC01539	ENST00000650203.1		n.1463-340G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81226 AN: 151750 Hom.: 22673 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.535 AC: 81313 AN: 151868 Hom.: 22705 Cov.: 32 AF XY: 0.533 AC XY: 39534 AN XY: 74200

African (AFR) AF: 0.708 AC: 29335 AN: 41446

American (AMR) AF: 0.565 AC: 8603 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2122 AN: 5168

South Asian (SAS) AF: 0.430 AC: 2065 AN: 4806

European-Finnish (FIN) AF: 0.408 AC: 4287 AN: 10520

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31650 AN: 67912

Other (OTH) AF: 0.523 AC: 1102 AN: 2106

Alfa AF: 0.519 Hom.: 3672

Bravo AF: 0.554

Asia WGS AF: 0.495 AC: 1716 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	11
DANN	Benign	0.40
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2646965; hg19: chr18-53692966;