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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902693	XM_047427980.1	c.*1057+10222G>A		intron_variant	Intron 3 of 6		XP_047283936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;