6-11084321-G-C

Variant names:

• chr6-11084321-G-C
• rs4713169

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 0.455 in 152,072 control chromosomes in the GnomAD database, including 16,780 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 0.45 (16780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69120 AN: 151954 Hom.: 16753 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.455 AC: 69184 AN: 152072 Hom.: 16780 Cov.: 32 AF XY: 0.464 AC XY: 34516 AN XY: 74332

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.472

Alfa AF: 0.437 Hom.: 1851

Bravo AF: 0.459

Asia WGS AF: 0.710 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713169; hg19: chr6-11084554;