11-1060419-G-C

Variant names:

• chr11-1060419-G-C
• rs7119740
• XR_001748091.2:n.3441C>G

Variant summary

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

The XR_001748091.2(LOC107987157):​n.3441C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,292 control chromosomes in the GnomAD database, including 1,165 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 0.11 (1165 hom., cov: 33)
• Consequence: LOC107987157 XR_001748091.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 2 publications found

Genes affected

LOC107987157 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.234 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: 0.107 AC: 16318 AN: 152174 Hom.: 1164 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.0761

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.107 AC: 16345 AN: 152292 Hom.: 1165 Cov.: 33 AF XY: 0.106 AC XY: 7916 AN XY: 74468

African (AFR) AF: 0.168 AC: 6966 AN: 41556

American (AMR) AF: 0.142 AC: 2170 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1273 AN: 5184

South Asian (SAS) AF: 0.0753 AC: 363 AN: 4820

European-Finnish (FIN) AF: 0.0626 AC: 665 AN: 10624

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0631 AC: 4294 AN: 68022

Other (OTH) AF: 0.105 AC: 221 AN: 2110

Alfa AF: 0.0297 Hom.: 24

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7119740; hg19: chr11-1060419;