rs4351280

chr6-136556908-A-Gchr6-136556908-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 0.209 in 151,976 control chromosomes in the GnomAD database, including 3,935 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 0.21 (3935 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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: 0.209 AC: 31686 AN: 151858 Hom.: 3913 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.215

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.209 AC: 31761 AN: 151976 Hom.: 3935 Cov.: 32 AF XY: 0.206 AC XY: 15295 AN XY: 74280

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.219

Alfa AF: 0.178 Hom.: 474

Bravo AF: 0.224

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4351280; hg19: chr6-136878046;