rs6923490

Variant names:

• chr6-104900830-C-T
• rs6923490
• ENST00000636951.1:n.458+25754G>A

Variant summary

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

The ENST00000636951.1(LIN28B-AS1):​n.458+25754G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIN28B-AS1	ENST00000636951.1	n.458+25754G>A		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.221 AC: 9175 AN: 41476

American (AMR) AF: 0.218 AC: 3338 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1234 AN: 5172

South Asian (SAS) AF: 0.168 AC: 808 AN: 4822

European-Finnish (FIN) AF: 0.219 AC: 2317 AN: 10590

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15411 AN: 67996

Other (OTH) AF: 0.220 AC: 465 AN: 2110

Alfa AF: 0.221 Hom.: 15791

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

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