rs363324

chr10-117229651-G-Achr10-117229651-G-Cchr10-117229651-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/exons	MANE	UniProt

Ensembl

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