rs10070224

Variant names:

• chr5-156918724-T-C
• rs10070224

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 0.301 in 150,170 control chromosomes in the GnomAD database, including 8,043 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 0.30 (8043 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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: 0.300 AC: 45048 AN: 150052 Hom.: 8013 Cov.: 29

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.301 AC: 45131 AN: 150170 Hom.: 8043 Cov.: 29 AF XY: 0.295 AC XY: 21591 AN XY: 73248

African (AFR) AF: 0.487 AC: 19762 AN: 40588

American (AMR) AF: 0.349 AC: 5194 AN: 14896

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 853 AN: 3460

East Asian (EAS) AF: 0.172 AC: 886 AN: 5140

South Asian (SAS) AF: 0.186 AC: 878 AN: 4724

European-Finnish (FIN) AF: 0.159 AC: 1651 AN: 10366

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14883 AN: 67722

Other (OTH) AF: 0.304 AC: 630 AN: 2070

Alfa AF: 0.251 Hom.: 22678

Bravo AF: 0.332

Asia WGS AF: 0.198 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.37
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs10070224; hg19: chr5-156345735; COSMIC: COSV50854406;