rs10485311

Positions:

• chr6-104890921-T-C

Variant summary

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

The ENST00000636951.1(LIN28B-AS1):​n.459-25834A>G 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 0.0545 in 152,236 control chromosomes in the GnomAD database, including 242 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 0.055 (242 hom., cov: 31)
• Consequence: LIN28B-AS1 ENST00000636951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901

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 (SAS) allele frequency at 95% confidence interval = 0.0702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIN28B-AS1	ENST00000636951.1	n.459-25834A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8311 AN: 152118 Hom.: 243 Cov.: 31

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0545 AC: 8304 AN: 152236 Hom.: 242 Cov.: 31 AF XY: 0.0553 AC XY: 4119 AN XY: 74444

Gnomad4 AFR AF: 0.0427

Gnomad4 AMR AF: 0.0428

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.0287

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.0496

Alfa AF: 0.0599 Hom.: 155

Bravo AF: 0.0509

Asia WGS AF: 0.0580 AC: 201 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	4.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485311; hg19: chr6-105338796;