6-13992854-A-G

Variant names:

• chr6-13992854-A-G
• rs12333130

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 0.371 in 151,784 control chromosomes in the GnomAD database, including 10,523 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 0.37 (10523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 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: 0.371 AC: 56230 AN: 151666 Hom.: 10508 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.371 AC: 56281 AN: 151784 Hom.: 10523 Cov.: 31 AF XY: 0.372 AC XY: 27557 AN XY: 74162

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.394

Alfa AF: 0.380 Hom.: 2631

Bravo AF: 0.365

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.94
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12333130; hg19: chr6-13993085;