rs4925858

Variant names:

• chr8-144446548-G-A
• rs4925858

Your query was ambiguous. Multiple possible variants found:

• chr8-144446548-G-A
• chr8-144446548-G-T

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 0.438 in 152,166 control chromosomes in the GnomAD database, including 14,878 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 0.44 (14878 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 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: 0.438 AC: 66656 AN: 152048 Hom.: 14886 Cov.: 34

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.438 AC: 66675 AN: 152166 Hom.: 14878 Cov.: 34 AF XY: 0.439 AC XY: 32691 AN XY: 74390

African (AFR) AF: 0.383 AC: 15880 AN: 41510

American (AMR) AF: 0.407 AC: 6236 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1965 AN: 5184

South Asian (SAS) AF: 0.582 AC: 2811 AN: 4826

European-Finnish (FIN) AF: 0.510 AC: 5406 AN: 10592

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31508 AN: 67966

Other (OTH) AF: 0.441 AC: 930 AN: 2108

Alfa AF: 0.455 Hom.: 2481

Bravo AF: 0.427

Asia WGS AF: 0.498 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs4925858; hg19: chr8-145671931;