XR_007064106.1:n.1276-3053T>C

Variant names:

• chr14-30389183-A-G
• rs17096653
• XR_007064106.1:n.1276-3053T>C

Variant summary

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

The XR_007064106.1(LOC112267868):​n.1276-3053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,174 control chromosomes in the GnomAD database, including 1,240 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 0.11 (1240 hom., cov: 32)
• Consequence: LOC112267868 XR_007064106.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 1 publications found

Genes affected

LOC112267868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267868	XR_007064106.1	n.1276-3053T>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16764 AN: 152056 Hom.: 1231 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.110 AC: 16786 AN: 152174 Hom.: 1240 Cov.: 32 AF XY: 0.109 AC XY: 8142 AN XY: 74422

African (AFR) AF: 0.171 AC: 7099 AN: 41454

American (AMR) AF: 0.0794 AC: 1215 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3468

East Asian (EAS) AF: 0.171 AC: 886 AN: 5180

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4824

European-Finnish (FIN) AF: 0.0324 AC: 344 AN: 10616

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5240 AN: 68020

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.0991 Hom.: 377

Bravo AF: 0.114

Asia WGS AF: 0.217 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs17096653; hg19: chr14-30858389;