5-4198432-T-C

Position:

• chr5-4198432-T-C

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 0.938 in 152,120 control chromosomes in the GnomAD database, including 67,087 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 0.94 (67087 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.938 AC: 142626 AN: 152002 Hom.: 67053 Cov.: 30

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.938 AC: 142711 AN: 152120 Hom.: 67087 Cov.: 30 AF XY: 0.939 AC XY: 69851 AN XY: 74358

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.930

Alfa AF: 0.948 Hom.: 10525

Bravo AF: 0.936

Asia WGS AF: 0.916 AC: 3186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6555262; hg19: chr5-4198545;