rs7114014

Variant names:

• chr11-65814301-C-T
• rs7114014
• XM_047427980.1:c.*1057+10222G>A

Variant summary

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

The XM_047427980.1(LOC124902693):​c.*1057+10222G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,112 control chromosomes in the GnomAD database, including 22,784 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 0.52 (22784 hom., cov: 33)
• Consequence: LOC124902693 XM_047427980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 6 publications found

Genes affected

LOC124902693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79035 AN: 151994 Hom.: 22781 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.520 AC: 79056 AN: 152112 Hom.: 22784 Cov.: 33 AF XY: 0.523 AC XY: 38875 AN XY: 74358

African (AFR) AF: 0.277 AC: 11481 AN: 41486

American (AMR) AF: 0.467 AC: 7139 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1771 AN: 5176

South Asian (SAS) AF: 0.616 AC: 2968 AN: 4822

European-Finnish (FIN) AF: 0.684 AC: 7242 AN: 10594

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44511 AN: 67980

Other (OTH) AF: 0.549 AC: 1157 AN: 2106

Alfa AF: 0.617 Hom.: 35855

Bravo AF: 0.486

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7114014; hg19: chr11-65581772;