4-45182425-G-A

Variant names:

• chr4-45182425-G-A
• rs348495

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 0.486 in 151,776 control chromosomes in the GnomAD database, including 19,062 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 (19062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73669 AN: 151658 Hom.: 19032 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.486 AC: 73755 AN: 151776 Hom.: 19062 Cov.: 32 AF XY: 0.480 AC XY: 35605 AN XY: 74166

African (AFR) AF: 0.659 AC: 27294 AN: 41442

American (AMR) AF: 0.430 AC: 6545 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1238 AN: 3460

East Asian (EAS) AF: 0.669 AC: 3460 AN: 5170

South Asian (SAS) AF: 0.346 AC: 1667 AN: 4814

European-Finnish (FIN) AF: 0.346 AC: 3653 AN: 10556

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.419 AC: 28418 AN: 67830

Other (OTH) AF: 0.475 AC: 999 AN: 2102

Alfa AF: 0.457 Hom.: 24209

Bravo AF: 0.503

Asia WGS AF: 0.553 AC: 1917 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.13
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs348495; hg19: chr4-45184442;