rs10072476

Variant names:

• chr5-44299298-C-T
• rs10072476

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 0.454 in 151,918 control chromosomes in the GnomAD database, including 17,586 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 0.45 (17586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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: 0.454 AC: 68931 AN: 151798 Hom.: 17542 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.454 AC: 69033 AN: 151918 Hom.: 17586 Cov.: 32 AF XY: 0.452 AC XY: 33583 AN XY: 74260

African (AFR) AF: 0.690 AC: 28614 AN: 41462

American (AMR) AF: 0.516 AC: 7870 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1118 AN: 3462

East Asian (EAS) AF: 0.510 AC: 2626 AN: 5152

South Asian (SAS) AF: 0.399 AC: 1926 AN: 4824

European-Finnish (FIN) AF: 0.326 AC: 3437 AN: 10556

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22112 AN: 67910

Other (OTH) AF: 0.431 AC: 907 AN: 2106

Alfa AF: 0.348 Hom.: 4263

Bravo AF: 0.481

Asia WGS AF: 0.525 AC: 1824 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10072476; hg19: chr5-44299400;