rs10484320

chr6-6010204-C-T

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 0.201 in 152,226 control chromosomes in the GnomAD database, including 3,321 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 0.20 (3321 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30550 AN: 152108 Hom.: 3315 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0784

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.201 AC: 30590 AN: 152226 Hom.: 3321 Cov.: 33 AF XY: 0.196 AC XY: 14596 AN XY: 74410

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.204

Alfa AF: 0.200 Hom.: 1957

Bravo AF: 0.201

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	9.8
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484320; hg19: chr6-6010437;