rs1364043

Variant names:

• chr5-63955024-T-G
• rs1364043

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 0.248 in 152,040 control chromosomes in the GnomAD database, including 5,130 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 0.25 (5130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 40 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 = 0.609 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37650 AN: 151920 Hom.: 5119 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.248 AC: 37662 AN: 152040 Hom.: 5130 Cov.: 32 AF XY: 0.252 AC XY: 18717 AN XY: 74298

African (AFR) AF: 0.211 AC: 8744 AN: 41492

American (AMR) AF: 0.251 AC: 3841 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3472

East Asian (EAS) AF: 0.627 AC: 3224 AN: 5144

South Asian (SAS) AF: 0.369 AC: 1775 AN: 4810

European-Finnish (FIN) AF: 0.224 AC: 2369 AN: 10574

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15741 AN: 67950

Other (OTH) AF: 0.249 AC: 527 AN: 2116

Alfa AF: 0.243 Hom.: 21258

Bravo AF: 0.245

Asia WGS AF: 0.481 AC: 1672 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	0.010
DANN	Benign	0.44
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1364043; hg19: chr5-63250851;