rs2318144

Positions:

• chr8-57202184-G-A

Variant summary

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

The ENST00000655105.1(LINC01606):​n.476+8173G>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 0.112 in 152,170 control chromosomes in the GnomAD database, including 994 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 0.11 (994 hom., cov: 32)
• Consequence: LINC01606 ENST00000655105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

Genes affected

LINC01606 (HGNC:51656): (long intergenic non-protein coding RNA 1606)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01606	ENST00000655105.1	n.476+8173G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17088 AN: 152052 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.112 AC: 17110 AN: 152170 Hom.: 994 Cov.: 32 AF XY: 0.112 AC XY: 8353 AN XY: 74396

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0723

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.113

Alfa AF: 0.130 Hom.: 934

Bravo AF: 0.109

Asia WGS AF: 0.102 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2318144; hg19: chr8-58114743;