6-159862407-A-C

Variant names:

• chr6-159862407-A-C
• rs6930229

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 0.637 in 151,962 control chromosomes in the GnomAD database, including 31,180 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 0.64 (31180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96767 AN: 151846 Hom.: 31175 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.637 AC: 96798 AN: 151962 Hom.: 31180 Cov.: 31 AF XY: 0.629 AC XY: 46734 AN XY: 74272

African (AFR) AF: 0.633 AC: 26219 AN: 41438

American (AMR) AF: 0.596 AC: 9102 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3472

East Asian (EAS) AF: 0.346 AC: 1786 AN: 5166

South Asian (SAS) AF: 0.656 AC: 3156 AN: 4812

European-Finnish (FIN) AF: 0.580 AC: 6113 AN: 10546

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45991 AN: 67946

Other (OTH) AF: 0.655 AC: 1383 AN: 2112

Alfa AF: 0.661 Hom.: 25181

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.32
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6930229; hg19: chr6-160283439;