rs10484320

Variant names:

• chr6-6010204-C-T
• rs10484320

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 0.201 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.236 AC: 9783 AN: 41534

American (AMR) AF: 0.171 AC: 2619 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 626 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5190

South Asian (SAS) AF: 0.0788 AC: 381 AN: 4832

European-Finnish (FIN) AF: 0.198 AC: 2094 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14397 AN: 68004

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.201 Hom.: 2139

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
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs10484320; hg19: chr6-6010437;