XR_935583.2:n.277+10777T>A

Variant names:

• chr18-65487125-A-T
• rs4455070
• XR_935583.2:n.277+10777T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_935583.2(LOC105372169):​n.277+10777T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,880 control chromosomes in the GnomAD database, including 11,765 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 0.38 (11765 hom., cov: 32)
• Consequence: LOC105372169 XR_935583.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 3 publications found

Genes affected

LOC105372169 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372169	XR_935583.2	n.277+10777T>A		intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57738 AN: 151762 Hom.: 11761 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.380 AC: 57748 AN: 151880 Hom.: 11765 Cov.: 32 AF XY: 0.381 AC XY: 28265 AN XY: 74216

African (AFR) AF: 0.237 AC: 9805 AN: 41454

American (AMR) AF: 0.363 AC: 5532 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3063 AN: 5146

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4233 AN: 10554

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29573 AN: 67910

Other (OTH) AF: 0.397 AC: 833 AN: 2100

Alfa AF: 0.392 Hom.: 1492

Bravo AF: 0.377

Asia WGS AF: 0.433 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	7.3
DANN	Benign	0.82
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs4455070; hg19: chr18-63154361;