rs1523537

Positions:

• chr20-52679623-T-C

Variant summary

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

The ENST00000661770.1(ENSG00000232294):​n.379+2515T>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 0.424 in 152,010 control chromosomes in the GnomAD database, including 13,771 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 0.42 (13771 hom., cov: 32)
• Consequence: ENST00000661770.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372666	XR_007067652.1	n.1520-1782T>C		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754670.2	n.1483-1565T>C		intron_variant, non_coding_transcript_variant
LOC105372666	XR_007067653.1	n.846-1782T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661770.1	n.379+2515T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64352 AN: 151892 Hom.: 13756 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.424 AC: 64410 AN: 152010 Hom.: 13771 Cov.: 32 AF XY: 0.427 AC XY: 31704 AN XY: 74310

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.415

Alfa AF: 0.423 Hom.: 9579

Bravo AF: 0.411

Asia WGS AF: 0.523 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.85
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1523537; hg19: chr20-51296162;