20-48399072-A-G

Position:

• chr20-48399072-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_936812.3(LOC105372643):​n.2398A>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_936812.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

LOC105372643 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105372643	XR_001754655.2	n.2394A>G		non_coding_transcript_exon_variant	3/3
LOC105372643	XR_007067635.1	n.2181A>G		non_coding_transcript_exon_variant	4/4
LOC105372643	XR_007067636.1	n.2185A>G		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.535

Alfa AF: 0.467 Hom.: 22652

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4809688; hg19: chr20-47027815;