rs6940019

Variant names:

• chr6-14059659-G-C
• rs6940019

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;