rs4946651

Variant names:

• chr6-104921635-A-G
• rs4946651
• ENST00000636060.1:n.418+4949T>C

Variant summary

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

The ENST00000636060.1(LIN28B-AS1):​n.418+4949T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,150 control chromosomes in the GnomAD database, including 18,613 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 0.47 (18613 hom., cov: 33)
• Consequence: LIN28B-AS1 ENST00000636060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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	ENST00000636060.1	n.418+4949T>C		intron_variant	Intron 3 of 3	5
LIN28B-AS1	ENST00000636951.1	n.458+4949T>C		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71541 AN: 152032 Hom.: 18600 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.470 AC: 71573 AN: 152150 Hom.: 18613 Cov.: 33 AF XY: 0.474 AC XY: 35243 AN XY: 74382

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.532

Alfa AF: 0.523 Hom.: 12539

Bravo AF: 0.464

Asia WGS AF: 0.653 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4946651; hg19: chr6-105369510;