chr6-157690668-C-G

Variant names:

• chr6-157690668-C-G
• rs6903041

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.66 (29310 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 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: 0.663 AC: 88810 AN: 133958 Hom.: 29305 Cov.: 18

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.663 AC: 88832 AN: 134000 Hom.: 29310 Cov.: 18 AF XY: 0.665 AC XY: 42143 AN XY: 63348

African (AFR) AF: 0.627 AC: 21857 AN: 34868

American (AMR) AF: 0.697 AC: 8815 AN: 12644

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2184 AN: 3398

East Asian (EAS) AF: 0.694 AC: 3114 AN: 4490

South Asian (SAS) AF: 0.706 AC: 2845 AN: 4028

European-Finnish (FIN) AF: 0.614 AC: 4035 AN: 6576

Middle Eastern (MID) AF: 0.617 AC: 153 AN: 248

European-Non Finnish (NFE) AF: 0.677 AC: 44071 AN: 65100

Other (OTH) AF: 0.658 AC: 1175 AN: 1786

Alfa AF: 0.655 Hom.: 3910

Bravo AF: 0.663

Asia WGS AF: 0.708 AC: 2443 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.57
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs6903041; hg19: chr6-158111700;