chr18-53683207-A-G

Variant names:

• chr18-53683207-A-G
• rs9946886
• XR_007066375.1:n.66+60178T>C

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+60178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 150,428 control chromosomes in the GnomAD database, including 11,819 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 0.37 (11819 hom., cov: 31)
• Consequence: LOC124904304 XR_007066375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 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=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 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: 0.366 AC: 54948 AN: 150310 Hom.: 11791 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.366 AC: 55014 AN: 150428 Hom.: 11819 Cov.: 31 AF XY: 0.371 AC XY: 27225 AN XY: 73474

African (AFR) AF: 0.397 AC: 16364 AN: 41186

American (AMR) AF: 0.468 AC: 7018 AN: 15008

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1390 AN: 3450

East Asian (EAS) AF: 0.466 AC: 2386 AN: 5124

South Asian (SAS) AF: 0.499 AC: 2378 AN: 4768

European-Finnish (FIN) AF: 0.339 AC: 3522 AN: 10388

Middle Eastern (MID) AF: 0.384 AC: 109 AN: 284

European-Non Finnish (NFE) AF: 0.309 AC: 20782 AN: 67244

Other (OTH) AF: 0.372 AC: 774 AN: 2080

Alfa AF: 0.351 Hom.: 1992

Asia WGS AF: 0.463 AC: 1610 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.5
DANN	Benign	0.94
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9946886; hg19: chr18-51209577;