rs6923490

chr6-104900830-C-T

Variant summary

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

The ENST00000636951.1(LIN28B-AS1):n.458+25754G>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 0.221 in 152,128 control chromosomes in the GnomAD database, including 3,771 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 0.22 (3771 hom., cov: 32)
• Consequence: LIN28B-AS1 ENST00000636951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

Genes affected

LIN28B-AS1 (HGNC:21553): (LIN28B antisense RNA 1)

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 = 0.228 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
LIN28B-AS1	ENST00000636951.1	n.458+25754G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33557 AN: 152010 Hom.: 3767 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.221 AC: 33572 AN: 152128 Hom.: 3771 Cov.: 32 AF XY: 0.221 AC XY: 16441 AN XY: 74386

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.220

Alfa AF: 0.218 Hom.: 7442

Bravo AF: 0.222

Asia WGS AF: 0.175 AC: 609 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	1.2
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6923490; hg19: chr6-105348705; COSMIC: COSV60262579;