rs2585423

Positions:

• chr20-54186450-T-C

Variant summary

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

The XR_936882.4(LOC105372675):​n.275-2910T>C 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 0.101 in 152,138 control chromosomes in the GnomAD database, including 966 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 0.10 (966 hom., cov: 32)
• Consequence: LOC105372675 XR_936882.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

LOC105372675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372675	XR_936882.4	n.275-2910T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15417 AN: 152018 Hom.: 965 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.101 AC: 15423 AN: 152138 Hom.: 966 Cov.: 32 AF XY: 0.103 AC XY: 7647 AN XY: 74374

Gnomad4 AFR AF: 0.0330

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.112

Alfa AF: 0.121 Hom.: 2397

Bravo AF: 0.102

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2585423; hg19: chr20-52802989;