2-47402759-T-G

Variant names:

• chr2-47402759-T-G
• rs1863332

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Benign reviewed by expert panel B:2
• Conservation: PhyloP100: -0.443
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId is 90490.Status of the report is reviewed_by_expert_panel, 3 stars.
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.154 AC: 6380 AN: 41500

American (AMR) AF: 0.159 AC: 2429 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0878 AC: 305 AN: 3472

East Asian (EAS) AF: 0.147 AC: 760 AN: 5174

South Asian (SAS) AF: 0.143 AC: 688 AN: 4822

European-Finnish (FIN) AF: 0.135 AC: 1429 AN: 10574

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0855 AC: 5812 AN: 67968

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.0933 Hom.: 1247

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

Sep 05, 2013

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Benign

Review Status: reviewed by expert panel

Collection Method: research

MAF >1% -

not provided Benign:1

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.9
DANN	Benign	0.81
PhyloP100		-0.44
PromoterAI		-0.083	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1863332; hg19: chr2-47629898;