chr2-237478585-A-G

Position:

• chr2-237478585-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 0.37 in 152,086 control chromosomes in the GnomAD database, including 13,622 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 0.37 (13622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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: 0.370 AC: 56226 AN: 151968 Hom.: 13584 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.370 AC: 56322 AN: 152086 Hom.: 13622 Cov.: 32 AF XY: 0.364 AC XY: 27086 AN XY: 74360

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.345

Alfa AF: 0.255 Hom.: 11716

Bravo AF: 0.396

Asia WGS AF: 0.356 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.94
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7584330; hg19: chr2-238387228; COSMIC: COSV69623542;