1-190562869-C-T

Variant names:

• chr1-190562869-C-T
• rs814951

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 0.401 in 151,912 control chromosomes in the GnomAD database, including 13,078 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 0.40 (13078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 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: 0.401 AC: 60814 AN: 151794 Hom.: 13063 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.401 AC: 60846 AN: 151912 Hom.: 13078 Cov.: 31 AF XY: 0.397 AC XY: 29461 AN XY: 74234

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.462

Alfa AF: 0.457 Hom.: 8041

Bravo AF: 0.399

Asia WGS AF: 0.350 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs814951; hg19: chr1-190531999;