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
• Publications: 2 publications found

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

African (AFR) AF: 0.164 AC: 6823 AN: 41490

American (AMR) AF: 0.0704 AC: 1072 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3464

East Asian (EAS) AF: 0.0850 AC: 439 AN: 5166

South Asian (SAS) AF: 0.162 AC: 777 AN: 4808

European-Finnish (FIN) AF: 0.0836 AC: 885 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0710 AC: 4821 AN: 67932

Other (OTH) AF: 0.105 AC: 222 AN: 2110

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
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs10484429; hg19: chr6-48851550;