rs2277777

Positions:

• chr20-16590289-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_937285.3(LOC105372541):​n.1291A>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 0.469 in 151,838 control chromosomes in the GnomAD database, including 17,008 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 0.47 (17008 hom., cov: 32)
• Consequence: LOC105372541 XR_937285.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766

Genes affected

LOC105372541 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372541	XR_937285.3	n.1291A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71234 AN: 151720 Hom.: 17000 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.469 AC: 71280 AN: 151838 Hom.: 17008 Cov.: 32 AF XY: 0.473 AC XY: 35114 AN XY: 74200

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.438

Alfa AF: 0.467 Hom.: 22274

Bravo AF: 0.460

Asia WGS AF: 0.519 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2277777; hg19: chr20-16570934;