rs4925858

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.144446548G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.441

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4925858; hg19: chr8-145671931;