2-47402759-T-G

Position:

• chr2-47402759-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.119 in 152,092 control chromosomes in the GnomAD database, including 1,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency: Genomes: 𝑓 0.12 (1231 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Benign reviewed by expert panel B:2
• Conservation: PhyloP100: -0.443

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 2-47402759-T-G is Benign according to our data. Variant chr2-47402759-T-G is described in ClinVar as [Benign]. Clinvar id is 90490.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47402759-T-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47402759T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18093 AN: 151974 Hom.: 1224 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.119 AC: 18116 AN: 152092 Hom.: 1231 Cov.: 32 AF XY: 0.124 AC XY: 9231 AN XY: 74346

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0855

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0909 Hom.: 949

Bravo AF: 0.121

Asia WGS AF: 0.157 AC: 548 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome Benign:1

Benign, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

MAF >1% -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1863332; hg19: chr2-47629898;