rs1010284

Variant names:

• chr6-19851377-C-T
• rs1010284

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 0.0654 in 152,094 control chromosomes in the GnomAD database, including 586 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 0.065 (586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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 = 0.281 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: 0.0653 AC: 9926 AN: 151974 Hom.: 580 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0654 AC: 9948 AN: 152094 Hom.: 586 Cov.: 32 AF XY: 0.0669 AC XY: 4973 AN XY: 74356

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.0624

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0300

Gnomad4 OTH AF: 0.0569

Alfa AF: 0.0534 Hom.: 61

Bravo AF: 0.0758

Asia WGS AF: 0.185 AC: 642 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	0.012
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: rs1010284; hg19: chr6-19851608;