1-8152530-A-G

Variant names:

• chr1-8152530-A-G
• rs10864333

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 0.632 in 151,306 control chromosomes in the GnomAD database, including 30,643 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 0.63 (30643 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.744 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: 0.632 AC: 95594 AN: 151188 Hom.: 30609 Cov.: 28

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.632 AC: 95664 AN: 151306 Hom.: 30643 Cov.: 28 AF XY: 0.633 AC XY: 46776 AN XY: 73922

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.676

Alfa AF: 0.629 Hom.: 3616

Bravo AF: 0.642

Asia WGS AF: 0.701 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10864333; hg19: chr1-8212590;