11-68682862-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984343	XR_001748281.1	n.230+4979C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;