1-158506104-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 0.235 in 152,134 control chromosomes in the GnomAD database, including 4,420 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 0.23 (4420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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 (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.235 AC: 35674 AN: 152014 Hom.: 4418 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.235 AC: 35695 AN: 152134 Hom.: 4420 Cov.: 32 AF XY: 0.239 AC XY: 17793 AN XY: 74352

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.241

Alfa AF: 0.237 Hom.: 1056

Bravo AF: 0.235

Asia WGS AF: 0.298 AC: 1034 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12041363; hg19: chr1-158475894;