chr6-14059659-G-C

Variant names:

• chr6-14059659-G-C
• rs6940019

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.176 AC: 7323 AN: 41496

American (AMR) AF: 0.0626 AC: 958 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0401 AC: 193 AN: 4816

European-Finnish (FIN) AF: 0.0433 AC: 459 AN: 10604

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3759 AN: 68016

Other (OTH) AF: 0.0795 AC: 168 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs6940019; hg19: chr6-14059890;