rs79480871

chr2-24471603-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;