rs6555261

Positions:

• chr5-4198323-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 0.925 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;