1-190545053-T-C

Variant names:

• chr1-190545053-T-C
• rs814958

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 0.839 in 152,096 control chromosomes in the GnomAD database, including 53,728 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 0.84 (53728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127568 AN: 151978 Hom.: 53691 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.839 AC: 127650 AN: 152096 Hom.: 53728 Cov.: 32 AF XY: 0.839 AC XY: 62395 AN XY: 74340

African (AFR) AF: 0.815 AC: 33833 AN: 41512

American (AMR) AF: 0.775 AC: 11827 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3159 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4270 AN: 5134

South Asian (SAS) AF: 0.894 AC: 4316 AN: 4828

European-Finnish (FIN) AF: 0.846 AC: 8962 AN: 10590

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58479 AN: 67984

Other (OTH) AF: 0.845 AC: 1781 AN: 2108

Alfa AF: 0.849 Hom.: 113549

Bravo AF: 0.829

Asia WGS AF: 0.828 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.26
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs814958; hg19: chr1-190514183;