1-158506104-T-C

Variant names:

• chr1-158506104-T-C
• rs12041363

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.172 AC: 7148 AN: 41530

American (AMR) AF: 0.263 AC: 4016 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2028 AN: 5170

South Asian (SAS) AF: 0.222 AC: 1067 AN: 4810

European-Finnish (FIN) AF: 0.293 AC: 3093 AN: 10568

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16391 AN: 67988

Other (OTH) AF: 0.241 AC: 510 AN: 2112

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12041363; hg19: chr1-158475894;