rs2430420

Positions:

• chr2-10436100-G-A

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 0.436 in 152,132 control chromosomes in the GnomAD database, including 16,311 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 (16311 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10436100G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66304 AN: 152014 Hom.: 16288 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.436 AC: 66370 AN: 152132 Hom.: 16311 Cov.: 33 AF XY: 0.436 AC XY: 32427 AN XY: 74370

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.392

Alfa AF: 0.412 Hom.: 2507

Bravo AF: 0.433

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2430420; hg19: chr2-10576226;