8-37571473-G-A

Variant names:

• chr8-37571473-G-A
• rs12682266
• ENST00000517363.2:n.35-1480C>T

Variant summary

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

The ENST00000517363.2(LINC01605):​n.35-1480C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,952 control chromosomes in the GnomAD database, including 8,227 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 0.24 (8227 hom., cov: 32)
• Consequence: LINC01605 ENST00000517363.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 9 publications found

Genes affected

LINC01605 (HGNC:51654): (long intergenic non-protein coding RNA 1605)

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 = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517363.2. 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
	LINC01605	NR_170186.1		n.779+27588C>T		intron	N/A
	LINC01605	NR_170187.1		n.780-17316C>T		intron	N/A
	LINC01605	NR_170188.1		n.780-17316C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01605	ENST00000517363.2	TSL:3	n.35-1480C>T		intron	N/A
	LINC01605	ENST00000783999.1		n.338+27588C>T		intron	N/A
	LINC01605	ENST00000784000.1		n.34+27588C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36899 AN: 151836 Hom.: 8193 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.243 AC: 36991 AN: 151952 Hom.: 8227 Cov.: 32 AF XY: 0.242 AC XY: 17967 AN XY: 74282

African (AFR) AF: 0.569 AC: 23548 AN: 41378

American (AMR) AF: 0.242 AC: 3698 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3462

East Asian (EAS) AF: 0.491 AC: 2525 AN: 5138

South Asian (SAS) AF: 0.144 AC: 693 AN: 4812

European-Finnish (FIN) AF: 0.0693 AC: 734 AN: 10588

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0706 AC: 4801 AN: 67980

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.122 Hom.: 1552

Bravo AF: 0.274

Asia WGS AF: 0.347 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12682266; hg19: chr8-37428991;