rs7112267

Variant names:

• chr11-1056981-G-A
• rs7112267
• XM_047427955.1:c.*103G>A

Variant summary

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

The XM_047427955.1(LOC124902605):​c.*103G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,138 control chromosomes in the GnomAD database, including 818 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 0.090 (818 hom., cov: 33)
• Consequence: LOC124902605 XM_047427955.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 1 publications found

Genes affected

LOC124902605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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: 0.0898 AC: 13646 AN: 152020 Hom.: 819 Cov.: 33

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0897 AC: 13642 AN: 152138 Hom.: 818 Cov.: 33 AF XY: 0.0924 AC XY: 6869 AN XY: 74368

African (AFR) AF: 0.0276 AC: 1145 AN: 41508

American (AMR) AF: 0.0486 AC: 744 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1344 AN: 5188

South Asian (SAS) AF: 0.125 AC: 603 AN: 4820

European-Finnish (FIN) AF: 0.163 AC: 1723 AN: 10564

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7645 AN: 67976

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.105 Hom.: 333

Bravo AF: 0.0765

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.22
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7112267; hg19: chr11-1056981;