NM_001024674.3:c.19+274G>T

Variant names:

• chr14-74085267-G-T
• rs2239557
• NM_001024674.3:c.19+274G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001024674.3(LIN52):​c.19+274G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LIN52 NM_001024674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 22 publications found

Genes affected

LIN52 (HGNC:19856): (lin-52 DREAM MuvB core complex component) Predicted to be involved in transcription, DNA-templated. Predicted to be located in nucleoplasm. Predicted to be part of DRM complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIN52	NM_001024674.3	c.19+274G>T		intron_variant	Intron 1 of 5	ENST00000555028.7	NP_001019845.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIN52	ENST00000555028.7	c.19+274G>T		intron_variant	Intron 1 of 5	1	NM_001024674.3	ENSP00000451812.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 200604 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 100980

African (AFR) AF: 0.00 AC: 0 AN: 6246

American (AMR) AF: 0.00 AC: 0 AN: 5780

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8052

East Asian (EAS) AF: 0.00 AC: 0 AN: 19086

South Asian (SAS) AF: 0.00 AC: 0 AN: 1904

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 15538

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1098

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 129334

Other (OTH) AF: 0.00 AC: 0 AN: 13566

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 5186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.26
PhyloP100		-1.2
PromoterAI		0.038	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2239557; hg19: chr14-74551970;