rs2742416

Positions:

• chr3-45688625-G-A
• chr3-45688625-G-C

Variant summary

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

The NR_033947.1(LIMD1-AS1):​n.258C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,266 control chromosomes in the GnomAD database, including 64,504 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 0.92 (64476 hom., cov: 31)
  • Exomes 𝑓: 0.98 (28 hom.)
• Consequence: LIMD1-AS1 NR_033947.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.43

Genes affected

LIMD1-AS1 (HGNC:44107): (LIMD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIMD1-AS1	NR_033947.1	n.258C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIMD1-AS1	ENST00000658801.1	n.555C>T		non_coding_transcript_exon_variant	1/2
LIMD1-AS1	ENST00000429798.1	n.115+395C>T		intron_variant, non_coding_transcript_variant		1
LIMD1-AS1	ENST00000427644.1	n.258C>T		non_coding_transcript_exon_variant	1/2	3
LIMD1-AS1	ENST00000655322.1	n.576C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140003 AN: 152090 Hom.: 64436 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.926

GnomAD4 exome AF: 0.983 AC: 57 AN: 58 Hom.: 28 Cov.: 0 AF XY: 0.969 AC XY: 31 AN XY: 32

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.977

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.920 AC: 140101 AN: 152208 Hom.: 64476 Cov.: 31 AF XY: 0.922 AC XY: 68568 AN XY: 74406

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.926

Alfa AF: 0.924 Hom.: 63545

Bravo AF: 0.920

Asia WGS AF: 0.934 AC: 3249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.17
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2742416; hg19: chr3-45730117;