2-25343038-A-G

Variant names:

• chr2-25343038-A-G
• rs1550117

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.161
• Publications: 68 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.951 AC: 39414 AN: 41458

American (AMR) AF: 0.749 AC: 11444 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3468

East Asian (EAS) AF: 0.775 AC: 3968 AN: 5122

South Asian (SAS) AF: 0.926 AC: 4456 AN: 4812

European-Finnish (FIN) AF: 0.967 AC: 10252 AN: 10600

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63143 AN: 67952

Other (OTH) AF: 0.888 AC: 1874 AN: 2110

Alfa AF: 0.920 Hom.: 155614

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

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.68
PhyloP100		-0.16
PromoterAI		0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1550117; hg19: chr2-25565907;