rs4404252

chr2-36672356-G-Achr2-36672356-G-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 0.536 in 151,930 control chromosomes in the GnomAD database, including 22,088 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 0.54 (22088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81382 AN: 151814 Hom.: 22069 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.536 AC: 81429 AN: 151930 Hom.: 22088 Cov.: 32 AF XY: 0.538 AC XY: 40000 AN XY: 74300

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.535

Alfa AF: 0.437 Hom.: 1332

Bravo AF: 0.538

Asia WGS AF: 0.518 AC: 1800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4404252; hg19: chr2-36899499;