rs10484601

Variant names:

• chr6-148574837-C-T
• rs10484601

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 0.177 in 152,132 control chromosomes in the GnomAD database, including 2,448 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 0.18 (2448 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.177 AC: 26856 AN: 152012 Hom.: 2445 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.177 AC: 26885 AN: 152132 Hom.: 2448 Cov.: 33 AF XY: 0.174 AC XY: 12955 AN XY: 74366

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0971

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.206

Alfa AF: 0.179 Hom.: 2803

Bravo AF: 0.187

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484601; hg19: chr6-148895973;