rs12682266

chr8-37571473-G-Achr8-37571473-G-Cchr8-37571473-G-T

Variant summary

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

The NR_170186.1(LINC01605):n.779+27588C>T 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 0.243 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 NR_170186.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

LINC01605 (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 (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01605	NR_170186.1	n.779+27588C>T		intron_variant, non_coding_transcript_variant
LINC01605	NR_170187.1	n.780-17316C>T		intron_variant, non_coding_transcript_variant
LINC01605	NR_170188.1	n.780-17316C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0693

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.218

Alfa AF: 0.0853 Hom.: 452

Bravo AF: 0.274

Asia WGS AF: 0.347 AC: 1204 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	0.15
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12682266; hg19: chr8-37428991;