chr6-13992854-A-G

Position:

• chr6-13992854-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 0.371 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;