chr2-24770803-A-G

Position:

• chr2-24770803-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 0.0764 in 175,108 control chromosomes in the GnomAD database, including 636 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 0.075 (519 hom., cov: 32)
  • Exomes 𝑓: 0.087 (117 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 11380 AN: 152190 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0708

GnomAD4 exome AF: 0.0866 AC: 1975 AN: 22800 Hom.: 117 AF XY: 0.0886 AC XY: 925 AN XY: 10442

Gnomad4 AFR exome AF: 0.129

Gnomad4 AMR exome AF: 0.0882

Gnomad4 ASJ exome AF: 0.0385

Gnomad4 EAS exome AF: 0.191

Gnomad4 SAS exome AF: 0.0842

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0546

Gnomad4 OTH exome AF: 0.0601

GnomAD4 genome AF: 0.0748 AC: 11397 AN: 152308 Hom.: 519 Cov.: 32 AF XY: 0.0770 AC XY: 5734 AN XY: 74478

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0965

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0477

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0564 Hom.: 164

Bravo AF: 0.0775

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6724282; hg19: chr2-24993672;