rs627839

Variant names:

• chr1-182572946-G-T
• rs627839

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 0.456 in 151,952 control chromosomes in the GnomAD database, including 16,298 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 0.46 (16298 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 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: 0.456 AC: 69208 AN: 151834 Hom.: 16292 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.456 AC: 69227 AN: 151952 Hom.: 16298 Cov.: 31 AF XY: 0.457 AC XY: 33937 AN XY: 74278

African (AFR) AF: 0.411 AC: 17019 AN: 41404

American (AMR) AF: 0.383 AC: 5854 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1519 AN: 5150

South Asian (SAS) AF: 0.490 AC: 2362 AN: 4820

European-Finnish (FIN) AF: 0.605 AC: 6386 AN: 10556

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33369 AN: 67954

Other (OTH) AF: 0.454 AC: 959 AN: 2114

Alfa AF: 0.471 Hom.: 15454

Bravo AF: 0.431

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.85
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs627839; hg19: chr1-182542081;