1-160872059-C-T

Variant names:

• chr1-160872059-C-T
• rs12058717

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 0.0851 in 151,326 control chromosomes in the GnomAD database, including 1,656 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 0.085 (1656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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: 0.0849 AC: 12839 AN: 151226 Hom.: 1649 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0529

Gnomad FIN AF: 0.000583

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.00561

Gnomad OTH AF: 0.0558

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

GnomAD4 genome AF: 0.0851 AC: 12872 AN: 151326 Hom.: 1656 Cov.: 32 AF XY: 0.0840 AC XY: 6209 AN XY: 73894

African (AFR) AF: 0.278 AC: 11448 AN: 41178

American (AMR) AF: 0.0392 AC: 595 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3462

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5166

South Asian (SAS) AF: 0.0522 AC: 251 AN: 4806

European-Finnish (FIN) AF: 0.000583 AC: 6 AN: 10296

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.00561 AC: 381 AN: 67926

Other (OTH) AF: 0.0552 AC: 116 AN: 2100

Alfa AF: 0.0820 Hom.: 244

Bravo AF: 0.0943

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.43
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs12058717; hg19: chr1-160841849;