chr2-57438494-A-G

Position:

• chr2-57438494-A-G

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 0.267 in 151,500 control chromosomes in the GnomAD database, including 6,353 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 0.27 (6353 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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 (AFR) allele frequency at 95% confidence interval = 0.432 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: 0.267 AC: 40447 AN: 151382 Hom.: 6329 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.267 AC: 40510 AN: 151500 Hom.: 6353 Cov.: 31 AF XY: 0.265 AC XY: 19608 AN XY: 74004

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.0576

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.240

Alfa AF: 0.247 Hom.: 1385

Bravo AF: 0.267

Asia WGS AF: 0.198 AC: 688 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7557548; hg19: chr2-57665629;