XR_936718.3:n.1155+1446T>C

Variant names:

• chr20-40462874-A-G
• rs2902941
• XR_936718.3:n.1155+1446T>C

Variant summary

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

The XR_936718.3(LOC105372618):​n.1155+1446T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,998 control chromosomes in the GnomAD database, including 20,476 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 0.47 (20476 hom., cov: 32)
• Consequence: LOC105372618 XR_936718.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 23 publications found

Genes affected

LOC105372618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71708 AN: 151880 Hom.: 20419 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.473 AC: 71823 AN: 151998 Hom.: 20476 Cov.: 32 AF XY: 0.464 AC XY: 34450 AN XY: 74316

African (AFR) AF: 0.815 AC: 33805 AN: 41462

American (AMR) AF: 0.387 AC: 5914 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1470 AN: 5170

South Asian (SAS) AF: 0.426 AC: 2052 AN: 4814

European-Finnish (FIN) AF: 0.245 AC: 2583 AN: 10558

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23531 AN: 67928

Other (OTH) AF: 0.428 AC: 903 AN: 2112

Alfa AF: 0.381 Hom.: 6093

Bravo AF: 0.496

Asia WGS AF: 0.388 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.64
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2902941; hg19: chr20-39091514;