18-76779997-C-T

Variant names:

• chr18-76779997-C-T
• rs8088596
• XR_007066419.1:n.201-54G>A

Variant summary

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

The XR_007066419.1(LOC124904327):​n.201-54G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,022 control chromosomes in the GnomAD database, including 11,363 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 (11363 hom., cov: 32)
• Consequence: LOC124904327 XR_007066419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 0 publications found

Genes affected

LOC124904327 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 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: 0.367 AC: 55733 AN: 151904 Hom.: 11366 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.367 AC: 55737 AN: 152022 Hom.: 11363 Cov.: 32 AF XY: 0.366 AC XY: 27168 AN XY: 74290

African (AFR) AF: 0.169 AC: 7020 AN: 41512

American (AMR) AF: 0.441 AC: 6728 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2016 AN: 5166

South Asian (SAS) AF: 0.413 AC: 1987 AN: 4814

European-Finnish (FIN) AF: 0.386 AC: 4070 AN: 10548

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31101 AN: 67928

Other (OTH) AF: 0.394 AC: 832 AN: 2112

Alfa AF: 0.430 Hom.: 55125

Bravo AF: 0.363

Asia WGS AF: 0.405 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.75
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs8088596; hg19: chr18-74491953;