rs10070224

Variant names:

• chr5-156918724-T-C
• rs10070224

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.304

Alfa AF: 0.243 Hom.: 10046

Bravo AF: 0.332

Asia WGS AF: 0.198 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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