XR_007066375.1:n.66+51574C>T

Variant names:

• chr18-53691811-G-A
• rs9965852
• XR_007066375.1:n.66+51574C>T

Variant summary

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

The XR_007066375.1(LOC124904304):​n.66+51574C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,880 control chromosomes in the GnomAD database, including 12,220 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 0.40 (12220 hom., cov: 32)
• Consequence: LOC124904304 XR_007066375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 2 publications found

Genes affected

LOC124904304 (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 (SAS) allele frequency at 95% confidence interval = 0.494 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: 0.398 AC: 60392 AN: 151762 Hom.: 12195 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.398 AC: 60455 AN: 151880 Hom.: 12220 Cov.: 32 AF XY: 0.403 AC XY: 29889 AN XY: 74226

African (AFR) AF: 0.409 AC: 16939 AN: 41398

American (AMR) AF: 0.494 AC: 7541 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2519 AN: 5142

South Asian (SAS) AF: 0.511 AC: 2464 AN: 4826

European-Finnish (FIN) AF: 0.376 AC: 3953 AN: 10524

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24266 AN: 67942

Other (OTH) AF: 0.401 AC: 844 AN: 2106

Alfa AF: 0.399 Hom.: 2198

Bravo AF: 0.407

Asia WGS AF: 0.480 AC: 1671 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	1.1
DANN	Benign	0.46
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs9965852; hg19: chr18-51218181;