1-190559315-C-T

Variant names:

• chr1-190559315-C-T
• rs1501501

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 0.155 in 152,036 control chromosomes in the GnomAD database, including 1,932 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 0.16 (1932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23590 AN: 151918 Hom.: 1920 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.155 AC: 23621 AN: 152036 Hom.: 1932 Cov.: 32 AF XY: 0.156 AC XY: 11582 AN XY: 74284

African (AFR) AF: 0.125 AC: 5180 AN: 41506

American (AMR) AF: 0.200 AC: 3052 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3472

East Asian (EAS) AF: 0.168 AC: 865 AN: 5134

South Asian (SAS) AF: 0.146 AC: 702 AN: 4812

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10566

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11099 AN: 67962

Other (OTH) AF: 0.149 AC: 315 AN: 2108

Alfa AF: 0.171 Hom.: 426

Bravo AF: 0.161

Asia WGS AF: 0.152 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.56
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1501501; hg19: chr1-190528445;