XR_007060636.1:n.456-3537C>T

Variant names:

• chr7-52421612-C-T
• rs2159817
• XR_007060636.1:n.456-3537C>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.456-3537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,208 control chromosomes in the GnomAD database, including 487 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 0.050 (487 hom., cov: 32)
• Consequence: LOC124901810 XR_007060636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0496 AC: 7545 AN: 152090 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00945

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0497 AC: 7560 AN: 152208 Hom.: 487 Cov.: 32 AF XY: 0.0508 AC XY: 3778 AN XY: 74406

African (AFR) AF: 0.104 AC: 4333 AN: 41532

American (AMR) AF: 0.0359 AC: 549 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1585 AN: 5140

South Asian (SAS) AF: 0.0493 AC: 238 AN: 4826

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00945 AC: 643 AN: 68020

Other (OTH) AF: 0.0548 AC: 116 AN: 2116

Alfa AF: 0.0261 Hom.: 866

Bravo AF: 0.0563

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.029
DANN	Benign	0.52
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2159817; hg19: chr7-52489308;