chr11-2159566-C-A

Position:

• chr11-2159566-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_003512.4(INS-IGF2):​n.246+1219G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,172 control chromosomes in the GnomAD database, including 2,425 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (2425 hom., cov: 32)
• Consequence: INS-IGF2 NR_003512.4 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.76

Genes affected

INS-IGF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 11-2159566-C-A is Benign according to our data. Variant chr11-2159566-C-A is described in ClinVar as [Benign]. Clinvar id is 1275239.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INS-IGF2	NR_003512.4	n.246+1219G>T		intron_variant, non_coding_transcript_variant
INS-IGF2	NM_001042376.3	c.187+1219G>T		intron_variant			NP_001035835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26167 AN: 152056 Hom.: 2424 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0409

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.172 AC: 26167 AN: 152172 Hom.: 2425 Cov.: 32 AF XY: 0.167 AC XY: 12403 AN XY: 74410

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0408

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.147

Alfa AF: 0.193 Hom.: 382

Bravo AF: 0.170

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.039
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs3842755; hg19: chr11-2180796;