rs4809918

Positions:

• chr20-52684661-G-A

Variant summary

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

The ENST00000661770.1(ENSG00000232294):​n.380-414G>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 0.0436 in 152,194 control chromosomes in the GnomAD database, including 232 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 0.044 (232 hom., cov: 32)
• Consequence: ENST00000661770.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372666	XR_007067652.1	n.1666-414G>A		intron_variant, non_coding_transcript_variant
LOC105372666	XR_007067653.1	n.992-414G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661770.1	n.380-414G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0434 AC: 6598 AN: 152076 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0436 AC: 6636 AN: 152194 Hom.: 232 Cov.: 32 AF XY: 0.0459 AC XY: 3413 AN XY: 74408

Gnomad4 AFR AF: 0.0345

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0311

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0349 Hom.: 244

Bravo AF: 0.0503

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4809918; hg19: chr20-51301200;