XR_007064055.1:n.165+2626C>T

Variant names:

• chr14-19941099-G-A
• rs2792135
• XR_007064055.1:n.165+2626C>T

Variant summary

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

The XR_007064055.1(LOC124903278):​n.165+2626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 148,958 control chromosomes in the GnomAD database, including 4,680 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 0.31 (4680 hom., cov: 38)
• Consequence: LOC124903278 XR_007064055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 1 publications found

Genes affected

LOC124903278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 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: 0.307 AC: 45720 AN: 148836 Hom.: 4680 Cov.: 38

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.307 AC: 45724 AN: 148958 Hom.: 4680 Cov.: 38 AF XY: 0.308 AC XY: 22402 AN XY: 72840

African (AFR) AF: 0.109 AC: 4475 AN: 41160

American (AMR) AF: 0.325 AC: 4842 AN: 14886

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1390 AN: 3310

East Asian (EAS) AF: 0.227 AC: 1143 AN: 5036

South Asian (SAS) AF: 0.413 AC: 1931 AN: 4670

European-Finnish (FIN) AF: 0.396 AC: 4079 AN: 10296

Middle Eastern (MID) AF: 0.380 AC: 108 AN: 284

European-Non Finnish (NFE) AF: 0.402 AC: 26720 AN: 66386

Other (OTH) AF: 0.341 AC: 696 AN: 2044

Alfa AF: 0.365 Hom.: 995

Asia WGS AF: 0.338 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.45
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2792135; hg19: chr14-20409258;