rs6940019

Positions:

• chr6-14059659-G-C

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 0.0868 in 152,200 control chromosomes in the GnomAD database, including 797 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 (797 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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 (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.0867 AC: 13188 AN: 152082 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0407

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0868 AC: 13205 AN: 152200 Hom.: 797 Cov.: 32 AF XY: 0.0856 AC XY: 6373 AN XY: 74434

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0868

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0401

Gnomad4 FIN AF: 0.0433

Gnomad4 NFE AF: 0.0553

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0792 Hom.: 89

Bravo AF: 0.0908

Asia WGS AF: 0.0300 AC: 106 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	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6940019; hg19: chr6-14059890;