chr20-48551929-C-T

Position:

• chr20-48551929-C-T

Variant summary

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

The XR_936817.4(LOC105372646):​n.343-7594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,876 control chromosomes in the GnomAD database, including 33,143 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 0.65 (33143 hom., cov: 31)
• Consequence: LOC105372646 XR_936817.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

LOC105372646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372646	XR_936817.4	n.343-7594G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99274 AN: 151758 Hom.: 33095 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.654 AC: 99378 AN: 151876 Hom.: 33143 Cov.: 31 AF XY: 0.656 AC XY: 48692 AN XY: 74186

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.651

Alfa AF: 0.670 Hom.: 8742

Bravo AF: 0.652

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4810813; hg19: chr20-47168467;