rs1893679

chr11-68682862-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001748281.1(LOC107984343):n.230+4979C>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

Genes affected

LOC107984343 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984343	XR_001748281.1	n.230+4979C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.653

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893679; hg19: chr11-68450330;