chr6-142034354-A-G

Variant names:

• chr6-142034354-A-G
• rs4352696
• XR_001744394.2:n.89+1162A>G

Variant summary

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

The XR_001744394.2(LOC107986654):​n.89+1162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,144 control chromosomes in the GnomAD database, including 34,552 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 0.65 (34552 hom., cov: 33)
• Consequence: LOC107986654 XR_001744394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 1 publications found

Genes affected

LOC107986654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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: 0.653 AC: 99295 AN: 152026 Hom.: 34485 Cov.: 33

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.653 AC: 99425 AN: 152144 Hom.: 34552 Cov.: 33 AF XY: 0.659 AC XY: 49001 AN XY: 74358

African (AFR) AF: 0.873 AC: 36242 AN: 41526

American (AMR) AF: 0.707 AC: 10820 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3468

East Asian (EAS) AF: 0.881 AC: 4559 AN: 5174

South Asian (SAS) AF: 0.624 AC: 3005 AN: 4816

European-Finnish (FIN) AF: 0.590 AC: 6235 AN: 10564

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35359 AN: 67982

Other (OTH) AF: 0.644 AC: 1361 AN: 2114

Alfa AF: 0.624 Hom.: 9819

Bravo AF: 0.677

Asia WGS AF: 0.760 AC: 2640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.36
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs4352696; hg19: chr6-142355491;