chr11-68682862-G-C

Variant names:

• chr11-68682862-G-C
• rs1893679
• XR_001748281.1:n.230+4979C>G

Variant summary

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

The XR_001748281.1(LOC107984343):​n.230+4979C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,072 control chromosomes in the GnomAD database, including 33,892 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 (33892 hom., cov: 32)
• Consequence: LOC107984343 XR_001748281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 6 publications found

Genes affected

LOC107984343 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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: 0.650 AC: 98788 AN: 151954 Hom.: 33880 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.650 AC: 98824 AN: 152072 Hom.: 33892 Cov.: 32 AF XY: 0.662 AC XY: 49206 AN XY: 74340

African (AFR) AF: 0.420 AC: 17394 AN: 41462

American (AMR) AF: 0.703 AC: 10743 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2584 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4470 AN: 5158

South Asian (SAS) AF: 0.785 AC: 3787 AN: 4826

European-Finnish (FIN) AF: 0.876 AC: 9291 AN: 10606

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48358 AN: 67942

Other (OTH) AF: 0.653 AC: 1379 AN: 2112

Alfa AF: 0.675 Hom.: 4425

Bravo AF: 0.624

Asia WGS AF: 0.799 AC: 2781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1893679; hg19: chr11-68450330;