rs853366

Variant names:

• chr6-14140920-G-C
• rs853366

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 0.234 in 152,132 control chromosomes in the GnomAD database, including 4,556 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 0.23 (4556 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.234 AC: 35572 AN: 152012 Hom.: 4542 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.234 AC: 35643 AN: 152132 Hom.: 4556 Cov.: 31 AF XY: 0.233 AC XY: 17358 AN XY: 74378

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0862

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.257

Alfa AF: 0.220 Hom.: 505

Bravo AF: 0.240

Asia WGS AF: 0.131 AC: 458 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853366; hg19: chr6-14141151;