6-104916546-T-G

Variant summary

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

The ENST00000636951.1(LIN28B-AS1):n.458+10038A>C 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 0.471 in 151,870 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: 31)
• Consequence: LIN28B-AS1 ENST00000636951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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+10038A>C		intron_variant, non_coding_transcript_variant		5
LIN28B-AS1	ENST00000636060.1	n.418+10038A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71499 AN: 151752 Hom.: 18599 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.471 AC: 71533 AN: 151870 Hom.: 18613 Cov.: 31 AF XY: 0.475 AC XY: 35235 AN XY: 74232

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.532

Alfa AF: 0.522 Hom.: 10236

Bravo AF: 0.464

Asia WGS AF: 0.654 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11156429; hg19: chr6-105364421;