chr4-83532155-C-A

Variant names:

• chr4-83532155-C-A
• rs17355209

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 0.468 in 152,044 control chromosomes in the GnomAD database, including 17,039 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 0.47 (17039 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71151 AN: 151926 Hom.: 17042 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.468 AC: 71165 AN: 152044 Hom.: 17039 Cov.: 32 AF XY: 0.462 AC XY: 34349 AN XY: 74306

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.491

Alfa AF: 0.467 Hom.: 7679

Bravo AF: 0.467

Asia WGS AF: 0.335 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17355209; hg19: chr4-84453308;