rs350294

Positions:

• chr6-158099285-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 0.696 in 151,850 control chromosomes in the GnomAD database, including 38,213 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 0.70 (38201 hom., cov: 30)
  • Exomes 𝑓: 0.61 (12 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105592 AN: 151666 Hom.: 38161 Cov.: 30

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.663

GnomAD4 exome AF: 0.606 AC: 40 AN: 66 Hom.: 12 AF XY: 0.583 AC XY: 28 AN XY: 48

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 NFE exome AF: 0.586

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.696 AC: 105671 AN: 151784 Hom.: 38201 Cov.: 30 AF XY: 0.691 AC XY: 51235 AN XY: 74178

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.661

Alfa AF: 0.674 Hom.: 4430

Bravo AF: 0.691

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs350294; hg19: chr6-158520317;