rs1611192

chr6-29804102-A-Gchr6-29804102-A-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 0.197 in 288,962 control chromosomes in the GnomAD database, including 6,179 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 0.22 (3634 hom., cov: 32)
  • Exomes 𝑓: 0.18 (2545 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.217 AC: 32953 AN: 152056 Hom.: 3635 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.176 AC: 24032 AN: 136788 Hom.: 2545 AF XY: 0.179 AC XY: 12807 AN XY: 71608

Gnomad4 AFR exome AF: 0.197

Gnomad4 AMR exome AF: 0.193

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.0521

Gnomad4 SAS exome AF: 0.214

Gnomad4 FIN exome AF: 0.144

Gnomad4 NFE exome AF: 0.186

Gnomad4 OTH exome AF: 0.181

GnomAD4 genome AF: 0.217 AC: 32950 AN: 152174 Hom.: 3634 Cov.: 32 AF XY: 0.211 AC XY: 15715 AN XY: 74398

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0676

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.216

Alfa AF: 0.238 Hom.: 3295

Bravo AF: 0.222

Asia WGS AF: 0.132 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611192; hg19: chr6-29771879;