rs9307811

Positions:

• chr4-83002716-C-T

Variant summary

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

The NM_194282.4(LIN54):​c.-33+7768G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 151,968 control chromosomes in the GnomAD database, including 37,001 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 0.69 (37001 hom., cov: 31)
• Consequence: LIN54 NM_194282.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

LIN54 (HGNC:25397): (lin-54 DREAM MuvB core complex component) LIN54 is a component of the LIN, or DREAM, complex, an essential regulator of cell cycle genes (Schmit et al., 2009 [PubMed 19725879]).[supplied by OMIM, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIN54	NM_194282.4	c.-33+7768G>A		intron_variant		ENST00000340417.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIN54	ENST00000340417.8	c.-33+7768G>A		intron_variant		1	NM_194282.4	P4

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105036 AN: 151852 Hom.: 36971 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.692 AC: 105130 AN: 151968 Hom.: 37001 Cov.: 31 AF XY: 0.690 AC XY: 51262 AN XY: 74280

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.704

Alfa AF: 0.742 Hom.: 40144

Bravo AF: 0.691

Asia WGS AF: 0.643 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307811; hg19: chr4-83923869;