2-25343038-A-G

Position:

• chr2-25343038-A-G

Variant summary

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

The variant allele was found at a frequency of 0.913 in 152,016 control chromosomes in the GnomAD database, including 63,663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.91 (63663 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.161

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 2-25343038-A-G is Benign according to our data. Variant chr2-25343038-A-G is described in ClinVar as [Benign]. Clinvar id is 706983.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.25343038A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138644 AN: 151898 Hom.: 63616 Cov.: 29

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.913 AC: 138748 AN: 152016 Hom.: 63663 Cov.: 29 AF XY: 0.911 AC XY: 67663 AN XY: 74310

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.888

Alfa AF: 0.918 Hom.: 60088

Bravo AF: 0.897

Asia WGS AF: 0.822 AC: 2856 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Tatton-Brown-Rahman overgrowth syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 06, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1550117; hg19: chr2-25565907;