rs10067427

chr5-100006343-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;