rs526941

Variant names:

• chr11-125697644-C-A
• rs526941
• XR_007062934.1:n.5205C>A

Variant summary

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

The XR_007062934.1(LOC105369551):​n.5205C>A 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 0.119 in 152,226 control chromosomes in the GnomAD database, including 1,248 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 0.12 (1248 hom., cov: 32)
• Consequence: LOC105369551 XR_007062934.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 3 publications found

Genes affected

LOC105369551 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751925.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297941	ENST00000751925.1		n.341-12446G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18151 AN: 152108 Hom.: 1249 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.119 AC: 18155 AN: 152226 Hom.: 1248 Cov.: 32 AF XY: 0.119 AC XY: 8828 AN XY: 74434

African (AFR) AF: 0.0764 AC: 3175 AN: 41536

American (AMR) AF: 0.0822 AC: 1258 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3464

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5170

South Asian (SAS) AF: 0.175 AC: 842 AN: 4818

European-Finnish (FIN) AF: 0.0905 AC: 961 AN: 10614

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9912 AN: 68006

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.134 Hom.: 1575

Bravo AF: 0.116

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.36
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs526941; hg19: chr11-125567539;