rs2400707

Variant names:

• chr5-148825489-A-G
• rs2400707

Your query was ambiguous. Multiple possible variants found:

• chr5-148825489-A-G
• chr5-148825489-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.599 in 152,036 control chromosomes in the GnomAD database, including 27,773 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.60 (27773 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 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: 0.600 AC: 91077 AN: 151916 Hom.: 27754 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.627

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.599 AC: 91141 AN: 152034 Hom.: 27773 Cov.: 32 AF XY: 0.607 AC XY: 45107 AN XY: 74328

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.633

Alfa AF: 0.572 Hom.: 12139

Bravo AF: 0.601

Asia WGS AF: 0.750 AC: 2605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.25

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: rs2400707; hg19: chr5-148205052;