5-4201031-A-G

Variant names:

• chr5-4201031-A-G
• rs6894281

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 0.91 in 152,122 control chromosomes in the GnomAD database, including 63,475 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 0.91 (63475 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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: 0.910 AC: 138359 AN: 152004 Hom.: 63470 Cov.: 30

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.910 AC: 138413 AN: 152122 Hom.: 63475 Cov.: 30 AF XY: 0.912 AC XY: 67792 AN XY: 74360

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.902

Alfa AF: 0.931 Hom.: 10196

Bravo AF: 0.904

Asia WGS AF: 0.898 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6894281; hg19: chr5-4201144;