rs10067427

Variant names:

• chr5-100006343-A-G
• rs10067427

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 0.422 in 148,852 control chromosomes in the GnomAD database, including 15,132 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 0.42 (15132 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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: 0.422 AC: 62801 AN: 148752 Hom.: 15092 Cov.: 25

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.422 AC: 62881 AN: 148852 Hom.: 15132 Cov.: 25 AF XY: 0.415 AC XY: 30064 AN XY: 72452

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.435

Alfa AF: 0.361 Hom.: 19702

Bravo AF: 0.446

Asia WGS AF: 0.248 AC: 864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10067427; hg19: chr5-99342047;