7-52381925-A-T

Variant names:

• chr7-52381925-A-T
• rs12718627
• XR_007060636.1:n.369-34008A>T

Variant summary

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

The XR_007060636.1(LOC124901810):​n.369-34008A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,036 control chromosomes in the GnomAD database, including 12,922 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 0.38 (12922 hom., cov: 32)
• Consequence: LOC124901810 XR_007060636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 1 publications found

Genes affected

LOC124901810 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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: 0.381 AC: 57923 AN: 151918 Hom.: 12924 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.381 AC: 57931 AN: 152036 Hom.: 12922 Cov.: 32 AF XY: 0.387 AC XY: 28739 AN XY: 74302

African (AFR) AF: 0.136 AC: 5626 AN: 41484

American (AMR) AF: 0.401 AC: 6117 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3468

East Asian (EAS) AF: 0.601 AC: 3096 AN: 5154

South Asian (SAS) AF: 0.494 AC: 2382 AN: 4820

European-Finnish (FIN) AF: 0.505 AC: 5336 AN: 10564

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32193 AN: 67962

Other (OTH) AF: 0.399 AC: 843 AN: 2112

Alfa AF: 0.410 Hom.: 1751

Bravo AF: 0.359

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.61
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs12718627; hg19: chr7-52449621;