rs10056388

Variant names:

• chr5-110169993-T-A
• rs10056388

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 0.5 in 152,002 control chromosomes in the GnomAD database, including 22,582 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 0.50 (22582 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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: 0.500 AC: 75952 AN: 151884 Hom.: 22589 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.500 AC: 75955 AN: 152002 Hom.: 22582 Cov.: 33 AF XY: 0.494 AC XY: 36696 AN XY: 74272

African (AFR) AF: 0.174 AC: 7209 AN: 41478

American (AMR) AF: 0.517 AC: 7887 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2545 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2092 AN: 5146

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4816

European-Finnish (FIN) AF: 0.610 AC: 6434 AN: 10548

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46042 AN: 67968

Other (OTH) AF: 0.540 AC: 1138 AN: 2108

Alfa AF: 0.585 Hom.: 3526

Bravo AF: 0.485

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.46
DANN	Benign	0.40
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10056388; hg19: chr5-109505694;