rs2396500

Variant names:

• chr2-227861148-A-G
• rs2396500

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 0.403 in 152,118 control chromosomes in the GnomAD database, including 13,360 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 0.40 (13360 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.529 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: 0.403 AC: 61326 AN: 152000 Hom.: 13364 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.403 AC: 61335 AN: 152118 Hom.: 13360 Cov.: 33 AF XY: 0.401 AC XY: 29830 AN XY: 74346

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.421

Alfa AF: 0.467 Hom.: 23223

Bravo AF: 0.409

Asia WGS AF: 0.444 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2396500; hg19: chr2-228725864;