5-4201618-G-T

Variant names:

• chr5-4201618-G-T
• rs6555263

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 0.901 in 151,822 control chromosomes in the GnomAD database, including 62,235 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 0.90 (62235 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 0.901 AC: 136739 AN: 151704 Hom.: 62217 Cov.: 30

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.901 AC: 136804 AN: 151822 Hom.: 62235 Cov.: 30 AF XY: 0.903 AC XY: 67009 AN XY: 74186

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.954

Gnomad4 OTH AF: 0.894

Alfa AF: 0.930 Hom.: 10206

Bravo AF: 0.893

Asia WGS AF: 0.893 AC: 3097 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6555263; hg19: chr5-4201731;