5-4197559-A-G

Variant names:

• chr5-4197559-A-G
• rs6555254

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 0.941 in 152,054 control chromosomes in the GnomAD database, including 67,472 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 (67472 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143038 AN: 151936 Hom.: 67437 Cov.: 29

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.961

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: 0.942

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

GnomAD4 genome AF: 0.941 AC: 143125 AN: 152054 Hom.: 67472 Cov.: 29 AF XY: 0.942 AC XY: 70026 AN XY: 74324

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.961

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: 0.933

Alfa AF: 0.952 Hom.: 8036

Bravo AF: 0.940

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.069
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6555254; hg19: chr5-4197672;