6-104916546-T-G

Variant names:

• chr6-104916546-T-G
• rs11156429
• ENST00000636060.1:n.418+10038A>C

Variant summary

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

The ENST00000636060.1(LIN28B-AS1):​n.418+10038A>C variant causes a intron 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 ENST00000636060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 22 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=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIN28B-AS1	ENST00000636060.1	n.418+10038A>C		intron_variant	Intron 3 of 3	5
LIN28B-AS1	ENST00000636951.1	n.458+10038A>C		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.228 AC: 9432 AN: 41400

American (AMR) AF: 0.583 AC: 8891 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3470

East Asian (EAS) AF: 0.694 AC: 3578 AN: 5152

South Asian (SAS) AF: 0.595 AC: 2862 AN: 4810

European-Finnish (FIN) AF: 0.559 AC: 5897 AN: 10550

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37048 AN: 67922

Other (OTH) AF: 0.532 AC: 1124 AN: 2114

Alfa AF: 0.502 Hom.: 17987

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11156429; hg19: chr6-105364421;