rs4492018

Positions:

• chr4-122593373-G-A

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 0.349 in 151,988 control chromosomes in the GnomAD database, including 9,924 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 0.35 (9924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53032 AN: 151866 Hom.: 9899 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.349 AC: 53096 AN: 151988 Hom.: 9924 Cov.: 32 AF XY: 0.353 AC XY: 26267 AN XY: 74308

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.371

Alfa AF: 0.312 Hom.: 4219

Bravo AF: 0.362

Asia WGS AF: 0.487 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.25
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4492018; hg19: chr4-123514528;