rs2585422

Positions:

• chr20-54187830-G-A
• chr20-54187830-G-C

Variant summary

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

The XR_936882.4(LOC105372675):​n.275-1530G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,276 control chromosomes in the GnomAD database, including 60,141 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 0.89 (60141 hom., cov: 32)
• Consequence: LOC105372675 XR_936882.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

Genes affected

LOC105372675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.275-1530G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134944 AN: 152158 Hom.: 60065 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.887 AC: 135082 AN: 152276 Hom.: 60141 Cov.: 32 AF XY: 0.883 AC XY: 65739 AN XY: 74430

Gnomad4 AFR AF: 0.972

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.871

Alfa AF: 0.864 Hom.: 112815

Bravo AF: 0.898

Asia WGS AF: 0.878 AC: 3053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2585422; hg19: chr20-52804369;