rs10484919

chr6-151653287-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 0.158 in 152,050 control chromosomes in the GnomAD database, including 2,787 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 0.16 (2787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

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 (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.158 AC: 23932 AN: 151932 Hom.: 2784 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.158 AC: 23952 AN: 152050 Hom.: 2787 Cov.: 32 AF XY: 0.153 AC XY: 11347 AN XY: 74336

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0334

Gnomad4 NFE AF: 0.0857

Gnomad4 OTH AF: 0.160

Alfa AF: 0.101 Hom.: 1999

Bravo AF: 0.170

Asia WGS AF: 0.205 AC: 712 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	4.9
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484919; hg19: chr6-151974422;