rs7114014

chr11-65814301-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124902693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902693	XM_047427980.1	c.*1057+10222G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.549

Alfa AF: 0.629 Hom.: 19815

Bravo AF: 0.486

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7114014; hg19: chr11-65581772;