rs342658

Variant names:

• chr6-123714119-G-A
• rs342658

Your query was ambiguous. Multiple possible variants found:

• chr6-123714119-G-A
• chr6-123714119-G-C

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 0.805 in 151,912 control chromosomes in the GnomAD database, including 52,233 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 0.80 (52233 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.94 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: 0.805 AC: 122203 AN: 151794 Hom.: 52227 Cov.: 30

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.805 AC: 122249 AN: 151912 Hom.: 52233 Cov.: 30 AF XY: 0.803 AC XY: 59612 AN XY: 74220

African (AFR) AF: 0.481 AC: 19888 AN: 41310

American (AMR) AF: 0.903 AC: 13793 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3188 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4673 AN: 5142

South Asian (SAS) AF: 0.889 AC: 4273 AN: 4808

European-Finnish (FIN) AF: 0.863 AC: 9133 AN: 10578

Middle Eastern (MID) AF: 0.894 AC: 261 AN: 292

European-Non Finnish (NFE) AF: 0.947 AC: 64367 AN: 68004

Other (OTH) AF: 0.846 AC: 1790 AN: 2116

Alfa AF: 0.875 Hom.: 95177

Bravo AF: 0.793

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.31
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs342658; hg19: chr6-124035264;