chr20-25237982-G-C

Position:

• chr20-25237982-G-C

Variant summary

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

The XR_001754564.3(LOC105372579):​n.6485C>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 0.389 in 152,062 control chromosomes in the GnomAD database, including 12,955 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 0.39 (12955 hom., cov: 32)
• Consequence: LOC105372579 XR_001754564.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

Genes affected

LOC105372579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372579	XR_001754564.3	n.6485C>G		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59118 AN: 151944 Hom.: 12956 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.389 AC: 59126 AN: 152062 Hom.: 12955 Cov.: 32 AF XY: 0.393 AC XY: 29171 AN XY: 74300

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.382

Alfa AF: 0.410 Hom.: 1676

Bravo AF: 0.376

Asia WGS AF: 0.651 AC: 2261 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.66
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6132819; hg19: chr20-25218618;