20-55853891-G-A

Variant names:

• chr20-55853891-G-A
• rs11907114
• XR_001754723.1:n.130-815G>A

Variant summary

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

The XR_001754723.1(LOC105372678):​n.130-815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,966 control chromosomes in the GnomAD database, including 8,696 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 0.33 (8696 hom., cov: 32)
• Consequence: LOC105372678 XR_001754723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 5 publications found

Genes affected

LOC105372678 (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 (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372678	XR_001754723.1	n.130-815G>A		intron_variant	Intron 1 of 2
LOC105372678	XR_001754724.1	n.130-815G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50374 AN: 151848 Hom.: 8695 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.332 AC: 50399 AN: 151966 Hom.: 8696 Cov.: 32 AF XY: 0.332 AC XY: 24677 AN XY: 74272

African (AFR) AF: 0.388 AC: 16090 AN: 41424

American (AMR) AF: 0.254 AC: 3875 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5180

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4816

European-Finnish (FIN) AF: 0.343 AC: 3617 AN: 10552

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22264 AN: 67946

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.330 Hom.: 25600

Bravo AF: 0.325

Asia WGS AF: 0.227 AC: 785 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.33
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs11907114; hg19: chr20-54428947;