rs10800309

Variant names:

• chr1-161502368-A-G
• rs10800309

Your query was ambiguous. Multiple possible variants found:

• chr1-161502368-A-G
• chr1-161502368-A-T

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 0.658 in 152,156 control chromosomes in the GnomAD database, including 33,717 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 0.66 (33717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.658 AC: 100031 AN: 152038 Hom.: 33689 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.658 AC: 100115 AN: 152156 Hom.: 33717 Cov.: 32 AF XY: 0.652 AC XY: 48500 AN XY: 74378

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.645

Alfa AF: 0.654 Hom.: 71013

Bravo AF: 0.664

Asia WGS AF: 0.437 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10800309; hg19: chr1-161472158;