chr18-76779997-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904327	XR_007066419.1	n.201-54G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;