chr3-5467360-A-G

Variant names:

• chr3-5467360-A-G
• rs10510308

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 0.057 in 152,164 control chromosomes in the GnomAD database, including 612 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 0.057 (612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 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: 0.0569 AC: 8652 AN: 152046 Hom.: 610 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0290

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00663

Gnomad OTH AF: 0.0432

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

GnomAD4 genome AF: 0.0570 AC: 8667 AN: 152164 Hom.: 612 Cov.: 32 AF XY: 0.0587 AC XY: 4368 AN XY: 74390

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0290

Gnomad4 NFE AF: 0.00665

Gnomad4 OTH AF: 0.0437

Alfa AF: 0.0354 Hom.: 44

Bravo AF: 0.0608

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.037
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510308; hg19: chr3-5509047;