1-169639679-C-T

Variant names:

• chr1-169639679-C-T
• rs1569476

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 0.343 in 151,984 control chromosomes in the GnomAD database, including 9,318 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 0.34 (9318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 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: 0.343 AC: 52055 AN: 151866 Hom.: 9318 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.343 AC: 52056 AN: 151984 Hom.: 9318 Cov.: 32 AF XY: 0.335 AC XY: 24880 AN XY: 74316

African (AFR) AF: 0.291 AC: 12043 AN: 41422

American (AMR) AF: 0.264 AC: 4023 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3468

East Asian (EAS) AF: 0.209 AC: 1084 AN: 5182

South Asian (SAS) AF: 0.253 AC: 1221 AN: 4824

European-Finnish (FIN) AF: 0.330 AC: 3483 AN: 10568

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27485 AN: 67942

Other (OTH) AF: 0.355 AC: 750 AN: 2114

Alfa AF: 0.384 Hom.: 41863

Bravo AF: 0.336

Asia WGS AF: 0.215 AC: 749 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1569476; hg19: chr1-169608917;