chr2-24471603-C-T

Variant names:

• chr2-24471603-C-T
• rs79480871

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 0.094 in 152,190 control chromosomes in the GnomAD database, including 782 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 0.094 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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: 0.0939 AC: 14286 AN: 152072 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0999

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.0940 AC: 14301 AN: 152190 Hom.: 782 Cov.: 32 AF XY: 0.0953 AC XY: 7092 AN XY: 74386

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0660

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0964

Alfa AF: 0.0742 Hom.: 169

Bravo AF: 0.0983

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79480871; hg19: chr2-24694472;