2-24397014-A-G

Position:

• chr2-24397014-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 0.576 in 152,114 control chromosomes in the GnomAD database, including 26,487 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 0.58 (26487 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24397014A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87571 AN: 151996 Hom.: 26487 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.576 AC: 87583 AN: 152114 Hom.: 26487 Cov.: 33 AF XY: 0.583 AC XY: 43337 AN XY: 74366

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.600

Alfa AF: 0.619 Hom.: 38992

Bravo AF: 0.566

Asia WGS AF: 0.687 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12470303; hg19: chr2-24619883;