5-4198323-T-C

Variant names:

• chr5-4198323-T-C
• rs6555261

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 0.925 in 152,226 control chromosomes in the GnomAD database, including 65,396 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 0.92 (65396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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: 0.925 AC: 140719 AN: 152106 Hom.: 65368 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.925 AC: 140799 AN: 152226 Hom.: 65396 Cov.: 32 AF XY: 0.926 AC XY: 68940 AN XY: 74432

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.920

Alfa AF: 0.948 Hom.: 64138

Bravo AF: 0.921

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6555261; hg19: chr5-4198436;