rs814951

chr1-190562869-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;