chr2-72037734-A-G

Variant names:

• chr2-72037734-A-G
• rs4852279

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 0.435 in 152,102 control chromosomes in the GnomAD database, including 14,525 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 0.44 (14525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 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: 0.435 AC: 66143 AN: 151984 Hom.: 14505 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.435 AC: 66207 AN: 152102 Hom.: 14525 Cov.: 33 AF XY: 0.435 AC XY: 32329 AN XY: 74344

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.446

Alfa AF: 0.447 Hom.: 27148

Bravo AF: 0.437

Asia WGS AF: 0.441 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4852279; hg19: chr2-72264864;