chr5-101401193-G-T

Variant names:

• chr5-101401193-G-T
• rs2400405

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 0.125 in 149,726 control chromosomes in the GnomAD database, including 2,585 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 0.13 (2585 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 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: 0.125 AC: 18696 AN: 149608 Hom.: 2577 Cov.: 28

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.00564

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.125 AC: 18738 AN: 149726 Hom.: 2585 Cov.: 28 AF XY: 0.124 AC XY: 9028 AN XY: 72990

African (AFR) AF: 0.331 AC: 13464 AN: 40692

American (AMR) AF: 0.185 AC: 2755 AN: 14876

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 142 AN: 3444

East Asian (EAS) AF: 0.0511 AC: 258 AN: 5048

South Asian (SAS) AF: 0.0497 AC: 238 AN: 4786

European-Finnish (FIN) AF: 0.00564 AC: 59 AN: 10470

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0238 AC: 1596 AN: 67124

Other (OTH) AF: 0.0999 AC: 208 AN: 2082

Alfa AF: 0.187 Hom.: 945

Bravo AF: 0.148

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.68
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2400405; hg19: chr5-100736897;