rs10484569

chr6-33091175-G-Achr6-33091175-G-Cchr6-33091175-G-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 0.062 in 152,190 control chromosomes in the GnomAD database, including 706 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 0.062 (706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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 = 0.401 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: 0.0618 AC: 9401 AN: 152072 Hom.: 694 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0613

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

GnomAD4 genome AF: 0.0620 AC: 9430 AN: 152190 Hom.: 706 Cov.: 32 AF XY: 0.0620 AC XY: 4611 AN XY: 74410

Gnomad4 AFR AF: 0.0837

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0357

Gnomad4 OTH AF: 0.0711

Alfa AF: 0.0342 Hom.: 128

Bravo AF: 0.0652

Asia WGS AF: 0.132 AC: 458 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	0.27
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484569; hg19: chr6-33058952;