rs10484429

Variant names:

• chr6-48883913-C-T
• rs10484429

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.101 in 151,998 control chromosomes in the GnomAD database, including 877 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 0.10 (877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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: 0.101 AC: 15270 AN: 151880 Hom.: 875 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.0850

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.101 AC: 15280 AN: 151998 Hom.: 877 Cov.: 32 AF XY: 0.102 AC XY: 7573 AN XY: 74292

Gnomad4 AFR AF: 0.164 AC: 0.164449 AN: 0.164449

Gnomad4 AMR AF: 0.0704 AC: 0.0703874 AN: 0.0703874

Gnomad4 ASJ AF: 0.0462 AC: 0.0461894 AN: 0.0461894

Gnomad4 EAS AF: 0.0850 AC: 0.0849787 AN: 0.0849787

Gnomad4 SAS AF: 0.162 AC: 0.161606 AN: 0.161606

Gnomad4 FIN AF: 0.0836 AC: 0.0835536 AN: 0.0835536

Gnomad4 NFE AF: 0.0710 AC: 0.070968 AN: 0.070968

Gnomad4 OTH AF: 0.105 AC: 0.105213 AN: 0.105213

Alfa AF: 0.0801 Hom.: 2328

Bravo AF: 0.102

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484429; hg19: chr6-48851550;