rs363324

Variant names:

• chr10-117229651-G-A
• rs363324

Your query was ambiguous. Multiple possible variants found:

• chr10-117229651-G-A
• chr10-117229651-G-C
• chr10-117229651-G-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 0.572 in 152,096 control chromosomes in the GnomAD database, including 27,868 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 0.57 (27868 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 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: 0.573 AC: 87021 AN: 151978 Hom.: 27866 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.572 AC: 87021 AN: 152096 Hom.: 27868 Cov.: 33 AF XY: 0.576 AC XY: 42817 AN XY: 74346

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.601

Alfa AF: 0.683 Hom.: 49178

Bravo AF: 0.542

Asia WGS AF: 0.379 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs363324; hg19: chr10-118989162;