1-190562869-C-T

Variant names:

• chr1-190562869-C-T
• rs814951

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 0.401 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.244 AC: 10132 AN: 41440

American (AMR) AF: 0.454 AC: 6928 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1969 AN: 3466

East Asian (EAS) AF: 0.331 AC: 1703 AN: 5140

South Asian (SAS) AF: 0.367 AC: 1765 AN: 4812

European-Finnish (FIN) AF: 0.397 AC: 4188 AN: 10556

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32756 AN: 67934

Other (OTH) AF: 0.462 AC: 974 AN: 2106

Alfa AF: 0.454 Hom.: 31166

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs814951; hg19: chr1-190531999;