rs78797168

Variant names:

• chr6-160038159-A-G
• rs78797168
• NM_000876.4:c.1316-2401A>G

Variant summary

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

The NM_000876.4(IGF2R):​c.1316-2401A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,216 control chromosomes in the GnomAD database, including 348 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 0.056 (348 hom., cov: 32)
• Consequence: IGF2R NM_000876.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 7 publications found

Genes affected

IGF2R (HGNC:5467): (insulin like growth factor 2 receptor) This gene encodes a receptor for both insulin-like growth factor 2 and mannose 6-phosphate. The binding sites for each ligand are located on different segments of the protein. This receptor has various functions, including in the intracellular trafficking of lysosomal enzymes, the activation of transforming growth factor beta, and the degradation of insulin-like growth factor 2. Mutation or loss of heterozygosity of this gene has been association with risk of hepatocellular carcinoma. The orthologous mouse gene is imprinted and shows exclusive expression from the maternal allele; however, imprinting of the human gene may be polymorphic, as only a minority of individuals showed biased expression from the maternal allele (PMID:8267611). [provided by RefSeq, Nov 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGF2R	NM_000876.4	c.1316-2401A>G		intron_variant	Intron 10 of 47	ENST00000356956.6	NP_000867.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGF2R	ENST00000356956.6	c.1316-2401A>G		intron_variant	Intron 10 of 47	1	NM_000876.4	ENSP00000349437.1
IGF2R	ENST00000676781.1	n.1316-2401A>G		intron_variant	Intron 10 of 48			ENSP00000504419.1
IGF2R	ENST00000677704.1	n.1316-2401A>G		intron_variant	Intron 10 of 48			ENSP00000503314.1

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 8555 AN: 152098 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0562 AC: 8550 AN: 152216 Hom.: 348 Cov.: 32 AF XY: 0.0573 AC XY: 4263 AN XY: 74434

African (AFR) AF: 0.0140 AC: 580 AN: 41532

American (AMR) AF: 0.0452 AC: 692 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1018 AN: 5170

South Asian (SAS) AF: 0.0953 AC: 459 AN: 4814

European-Finnish (FIN) AF: 0.0519 AC: 550 AN: 10606

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0722 AC: 4912 AN: 68010

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0661 Hom.: 133

Bravo AF: 0.0531

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs78797168; hg19: chr6-160459191;