11-68678956-C-T

Position:

• chr11-68678956-C-T

Variant summary

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

The XR_001748281.1(LOC107984343):​n.231-1966G>A 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 0.845 in 152,116 control chromosomes in the GnomAD database, including 54,420 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 0.85 (54420 hom., cov: 31)
• Consequence: LOC107984343 XR_001748281.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

Genes affected

LOC107984343 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984343	XR_001748281.1	n.231-1966G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128480 AN: 151998 Hom.: 54374 Cov.: 31

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.845 AC: 128587 AN: 152116 Hom.: 54420 Cov.: 31 AF XY: 0.849 AC XY: 63172 AN XY: 74368

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.828

Alfa AF: 0.818 Hom.: 98267

Bravo AF: 0.836

Asia WGS AF: 0.899 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187331; hg19: chr11-68446424;