rs6908732

Variant names:

• chr6-151631755-G-A
• rs6908732
• XR_007059816.1:n.4647G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-151631755-G-A
• chr6-151631755-G-C

Variant summary

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

The XR_007059816.1(LOC124901435):​n.4647G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,202 control chromosomes in the GnomAD database, including 49,308 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 (49308 hom., cov: 33)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 4 publications found

Genes affected

LOC124901435 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.919 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: 0.800 AC: 121617 AN: 152084 Hom.: 49267 Cov.: 33

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.800 AC: 121714 AN: 152202 Hom.: 49308 Cov.: 33 AF XY: 0.799 AC XY: 59418 AN XY: 74392

African (AFR) AF: 0.926 AC: 38490 AN: 41550

American (AMR) AF: 0.810 AC: 12396 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2397 AN: 3470

East Asian (EAS) AF: 0.912 AC: 4726 AN: 5182

South Asian (SAS) AF: 0.768 AC: 3701 AN: 4822

European-Finnish (FIN) AF: 0.679 AC: 7180 AN: 10570

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50168 AN: 67992

Other (OTH) AF: 0.804 AC: 1702 AN: 2116

Alfa AF: 0.764 Hom.: 165371

Bravo AF: 0.817

Asia WGS AF: 0.817 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.58
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs6908732; hg19: chr6-151952890; COSMIC: COSV60292427;