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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987157	XR_001748091.2	n.3441C>G		non_coding_transcript_exon_variant	Exon 5 of 5
LOC107987157	XR_007062544.1	n.3699C>G		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

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

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 v4.3

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;