rs3842756

chr11-2159542-C-T

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+1243G>A 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 0.171 in 152,174 control chromosomes in the GnomAD database, including 2,388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (2388 hom., cov: 33)
• Consequence: INS-IGF2 NR_003512.4 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.74

Genes affected

INS-IGF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 11-2159542-C-T is Benign according to our data. Variant chr11-2159542-C-T is described in ClinVar as [Benign]. Clinvar id is 1269776.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	UniProt
INS-IGF2	NR_003512.4	n.246+1243G>A		intron_variant, non_coding_transcript_variant
INS-IGF2	NM_001042376.3	c.187+1243G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26005 AN: 152056 Hom.: 2386 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0413

Gnomad SAS AF: 0.128

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: 0.171 AC: 26004 AN: 152174 Hom.: 2388 Cov.: 33 AF XY: 0.165 AC XY: 12304 AN XY: 74380

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0412

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.147

Alfa AF: 0.192 Hom.: 377

Bravo AF: 0.168

Asia WGS AF: 0.0950 AC: 332 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	-0.79
Cadd	Benign	4.1
Dann	Benign	0.65

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: rs3842756; hg19: chr11-2180772;