XR_001754655.2:n.2394A>G

Variant names:

• chr20-48399072-A-G
• rs4809688
• XR_001754655.2:n.2394A>G

Variant summary

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

The XR_001754655.2(LOC105372643):​n.2394A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,074 control chromosomes in the GnomAD database, including 25,258 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 0.55 (25258 hom., cov: 32)
• Consequence: LOC105372643 XR_001754655.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 3 publications found

Genes affected

LOC105372643 (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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372643	XR_001754655.2	n.2394A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105372643	XR_007067635.1	n.2181A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105372643	XR_007067636.1	n.2185A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105372643	XR_936812.3	n.2398A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84023 AN: 151956 Hom.: 25210 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.553 AC: 84138 AN: 152074 Hom.: 25258 Cov.: 32 AF XY: 0.546 AC XY: 40575 AN XY: 74340

African (AFR) AF: 0.783 AC: 32487 AN: 41510

American (AMR) AF: 0.617 AC: 9418 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3471 AN: 5156

South Asian (SAS) AF: 0.413 AC: 1990 AN: 4824

European-Finnish (FIN) AF: 0.328 AC: 3459 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29870 AN: 67972

Other (OTH) AF: 0.535 AC: 1127 AN: 2106

Alfa AF: 0.480 Hom.: 30589

Bravo AF: 0.593

Asia WGS AF: 0.543 AC: 1889 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	2.8
DANN	Benign	0.49
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs4809688; hg19: chr20-47027815;