chr5-4201031-A-G

Variant names:

• chr5-4201031-A-G
• rs6894281

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.789 AC: 32729 AN: 41470

American (AMR) AF: 0.946 AC: 14468 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3359 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5103 AN: 5134

South Asian (SAS) AF: 0.889 AC: 4280 AN: 4816

European-Finnish (FIN) AF: 0.985 AC: 10450 AN: 10610

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64964 AN: 68018

Other (OTH) AF: 0.902 AC: 1907 AN: 2114

Alfa AF: 0.934 Hom.: 21222

Bravo AF: 0.904

Asia WGS AF: 0.898 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs6894281; hg19: chr5-4201144;