1-24480070-T-C

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 0.241 in 146,342 control chromosomes in the GnomAD database, including 6,456 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 0.24 (6456 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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: 0.241 AC: 35306 AN: 146224 Hom.: 6447 Cov.: 28

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.241 AC: 35338 AN: 146342 Hom.: 6456 Cov.: 28 AF XY: 0.245 AC XY: 17408 AN XY: 71198

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.247

Alfa AF: 0.239 Hom.: 5206

Asia WGS AF: 0.394 AC: 1335 AN: 3400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.40
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs195738; hg19: chr1-24806560;