rs149970

chr6-28012442-G-A

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 0.243 in 488,550 control chromosomes in the GnomAD database, including 15,710 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 0.27 (6195 hom., cov: 32)
  • Exomes 𝑓: 0.23 (9515 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 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: 0.271 AC: 41227 AN: 151902 Hom.: 6172 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.230 AC: 77368 AN: 336528 Hom.: 9515 AF XY: 0.229 AC XY: 41022 AN XY: 179218

Gnomad4 AFR exome AF: 0.397

Gnomad4 AMR exome AF: 0.259

Gnomad4 ASJ exome AF: 0.190

Gnomad4 EAS exome AF: 0.245

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.230

GnomAD4 genome AF: 0.272 AC: 41302 AN: 152022 Hom.: 6195 Cov.: 32 AF XY: 0.265 AC XY: 19724 AN XY: 74328

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.257

Alfa AF: 0.243 Hom.: 603

Bravo AF: 0.285

Asia WGS AF: 0.229 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.70
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149970; hg19: chr6-27980220;