rs10485311

Variant names:

• chr6-104890921-T-C
• rs10485311
• ENST00000636951.1:n.459-25834A>G

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIN28B-AS1	ENST00000636951.1	n.459-25834A>G		intron_variant	Intron 3 of 4	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;