rs2742416

Variant names:

• chr3-45688625-G-A
• rs2742416
• ENST00000429798.1:n.115+395C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000429798.1(LIMD1-AS1):​n.115+395C>T variant causes a intron 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 ENST00000429798.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.43
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LIMD1-AS1	NR_033947.1	n.258C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIMD1-AS1	ENST00000429798.1	n.115+395C>T		intron_variant	Intron 1 of 1	1
LIMD1-AS1	ENST00000427644.1	n.258C>T		non_coding_transcript_exon_variant	Exon 1 of 2	3
LIMD1-AS1	ENST00000655322.1	n.576C>T		non_coding_transcript_exon_variant	Exon 1 of 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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 8 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.977 AC: 43 AN: 44

Other (OTH) AF: 1.00 AC: 2 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.908 AC: 37703 AN: 41526

American (AMR) AF: 0.954 AC: 14590 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3414 AN: 3470

East Asian (EAS) AF: 0.916 AC: 4739 AN: 5174

South Asian (SAS) AF: 0.974 AC: 4692 AN: 4818

European-Finnish (FIN) AF: 0.915 AC: 9683 AN: 10584

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62220 AN: 68028

Other (OTH) AF: 0.926 AC: 1953 AN: 2108

Alfa AF: 0.924 Hom.: 83540

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
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs2742416; hg19: chr3-45730117;