6-104931079-C-T

Variant names:

• chr6-104931079-C-T
• rs7759938
• ENST00000636060.1:n.120-4197G>A

Variant summary

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

The ENST00000636060.1(LIN28B-AS1):​n.120-4197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,040 control chromosomes in the GnomAD database, including 30,262 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 0.62 (30262 hom., cov: 32)
• Consequence: LIN28B-AS1 ENST00000636060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 118 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636060.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIN28B-AS1	ENST00000636060.1	TSL:5	n.120-4197G>A		intron	N/A
	LIN28B-AS1	ENST00000636951.1	TSL:5	n.160-4197G>A		intron	N/A
	LIN28B-AS1	ENST00000668527.1		n.244-4197G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94290 AN: 151922 Hom.: 30247 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.620 AC: 94339 AN: 152040 Hom.: 30262 Cov.: 32 AF XY: 0.623 AC XY: 46272 AN XY: 74310

African (AFR) AF: 0.447 AC: 18527 AN: 41470

American (AMR) AF: 0.705 AC: 10764 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2491 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3589 AN: 5156

South Asian (SAS) AF: 0.709 AC: 3423 AN: 4826

European-Finnish (FIN) AF: 0.680 AC: 7189 AN: 10566

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46034 AN: 67970

Other (OTH) AF: 0.664 AC: 1399 AN: 2106

Alfa AF: 0.667 Hom.: 140573

Bravo AF: 0.619

Asia WGS AF: 0.706 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.68
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs7759938; hg19: chr6-105378954;