rs10484461

Variant names:

• chr6-113406128-C-T
• rs10484461

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 0.128 in 152,090 control chromosomes in the GnomAD database, including 1,484 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 0.13 (1484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.128 AC: 19383 AN: 151972 Hom.: 1482 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0271

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.128 AC: 19399 AN: 152090 Hom.: 1484 Cov.: 32 AF XY: 0.125 AC XY: 9293 AN XY: 74370

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0270

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.109

Alfa AF: 0.115 Hom.: 201

Bravo AF: 0.126

Asia WGS AF: 0.0830 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484461; hg19: chr6-113727330;