rs1319898

Variant names:

• chr1-166037787-C-T
• rs1319898

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 0.489 in 151,988 control chromosomes in the GnomAD database, including 18,635 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 0.49 (18635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74321 AN: 151870 Hom.: 18626 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.489 AC: 74352 AN: 151988 Hom.: 18635 Cov.: 32 AF XY: 0.481 AC XY: 35769 AN XY: 74288

African (AFR) AF: 0.412 AC: 17051 AN: 41424

American (AMR) AF: 0.444 AC: 6786 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1420 AN: 5158

South Asian (SAS) AF: 0.529 AC: 2551 AN: 4824

European-Finnish (FIN) AF: 0.476 AC: 5016 AN: 10542

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 38041 AN: 67982

Other (OTH) AF: 0.492 AC: 1039 AN: 2112

Alfa AF: 0.536 Hom.: 54891

Bravo AF: 0.482

Asia WGS AF: 0.466 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Benign	0.57
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1319898; hg19: chr1-166007024;