2-102259127-A-G

Position:

• chr2-102259127-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 0.412 in 152,046 control chromosomes in the GnomAD database, including 14,451 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 0.41 (14451 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102259127A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62620 AN: 151926 Hom.: 14466 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.412 AC: 62623 AN: 152046 Hom.: 14451 Cov.: 32 AF XY: 0.421 AC XY: 31282 AN XY: 74302

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.394

Alfa AF: 0.439 Hom.: 1912

Bravo AF: 0.385

Asia WGS AF: 0.709 AC: 2463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1345301; hg19: chr2-102875587;