rs200146786

Variant names:

• chr12-102396788-CTTT-C
• rs200146786
• NM_000618.5:c.*5716_*5718delAAA

Your query was ambiguous. Multiple possible variants found:

• chr12-102396788-CTTT-C
• chr12-102396788-CTTT-CT
• chr12-102396788-CTTT-CTT
• chr12-102396788-CTTT-CTTTT
• chr12-102396788-CTTT-CTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000618.5(IGF1):​c.*5716_*5718delAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000847 in 377,684 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000021 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: IGF1 NM_000618.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

IGF1 (HGNC:5464): (insulin like growth factor 1) The protein encoded by this gene is similar to insulin in function and structure and is a member of a family of proteins involved in mediating growth and development. The encoded protein is processed from a precursor, bound by a specific receptor, and secreted. Defects in this gene are a cause of insulin-like growth factor I deficiency. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar processing to generate mature protein. [provided by RefSeq, Sep 2015]

HELLPAR (HGNC:43984): (HELLP associated long non-coding RNA)

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGF1	NM_000618.5	c.*5716_*5718delAAA		3_prime_UTR_variant	Exon 4 of 4	ENST00000337514.11	NP_000609.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGF1	ENST00000337514	c.*5716_*5718delAAA		3_prime_UTR_variant	Exon 4 of 4	1	NM_000618.5	ENSP00000337612.7
HELLPAR	ENST00000626826.1	n.199215_199217delTTT		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02456	ENST00000635615.1	n.450-26272_450-26270delTTT		intron_variant	Intron 4 of 5	5
LINC02456	ENST00000704346.1	n.1067-26272_1067-26270delTTT		intron_variant	Intron 9 of 10

Frequencies

GnomAD3 genomes AF: 0.0000208 AC: 3 AN: 144206 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000254

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000153

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000124 AC: 29 AN: 233478 Hom.: 0 AF XY: 0.000127 AC XY: 15 AN XY: 118402

Gnomad4 AFR exome AF: 0.000294

Gnomad4 AMR exome AF: 0.000141

Gnomad4 ASJ exome AF: 0.000228

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000706

Gnomad4 FIN exome AF: 0.000308

Gnomad4 NFE exome AF: 0.000107

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000208 AC: 3 AN: 144206 Hom.: 0 Cov.: 31 AF XY: 0.0000143 AC XY: 1 AN XY: 70096

Gnomad4 AFR AF: 0.0000254

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000112

Gnomad4 NFE AF: 0.0000153

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs200146786; hg19: chr12-102790566;