rs4084090

chr6-31251058-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 0.0867 in 152,190 control chromosomes in the GnomAD database, including 656 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 0.087 (656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

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 (SAS) allele frequency at 95% confidence interval = 0.132 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: 0.0866 AC: 13175 AN: 152072 Hom.: 650 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.108

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0867 AC: 13199 AN: 152190 Hom.: 656 Cov.: 32 AF XY: 0.0876 AC XY: 6516 AN XY: 74420

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0908

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.0746

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0740 Hom.: 162

Bravo AF: 0.0939

Asia WGS AF: 0.119 AC: 412 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	1.6
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4084090; hg19: chr6-31218835;