rs6820379

Positions:

• chr4-105120082-A-G

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 0.1 in 152,210 control chromosomes in the GnomAD database, including 1,459 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 0.10 (1459 hom., cov: 33)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 (AFR) allele frequency at 95% confidence interval = 0.253 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: 0.100 AC: 15236 AN: 152080 Hom.: 1455 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0783

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 NFE exome AF: 0.0833

GnomAD4 genome AF: 0.100 AC: 15256 AN: 152198 Hom.: 1459 Cov.: 33 AF XY: 0.0989 AC XY: 7358 AN XY: 74428

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.0452

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0775

Alfa AF: 0.0631 Hom.: 133

Bravo AF: 0.108

Asia WGS AF: 0.0270 AC: 96 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	0.24
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6820379; hg19: chr4-106041239;