rs1010824

chr8-107239685-G-A

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 0.147 in 151,778 control chromosomes in the GnomAD database, including 2,076 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 0.15 (2076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.147 AC: 22260 AN: 151662 Hom.: 2080 Cov.: 31

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.147 AC: 22258 AN: 151778 Hom.: 2076 Cov.: 31 AF XY: 0.153 AC XY: 11360 AN XY: 74138

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.160

Alfa AF: 0.159 Hom.: 372

Bravo AF: 0.140

Asia WGS AF: 0.251 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.042
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1010824; hg19: chr8-108251913;