rs1884136

Positions:

• chr20-10869816-G-T

Variant summary

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

The ENST00000605292.5(ENSG00000270792):​n.99-39010G>T 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 0.0865 in 152,148 control chromosomes in the GnomAD database, including 828 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 0.087 (828 hom., cov: 33)
• Consequence: ENST00000605292.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

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 = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000605292.5	n.99-39010G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000667822.1	n.332-39010G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13159 AN: 152030 Hom.: 827 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0911

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

GnomAD4 genome AF: 0.0865 AC: 13167 AN: 152148 Hom.: 828 Cov.: 33 AF XY: 0.0890 AC XY: 6621 AN XY: 74384

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.0657

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0719

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0920

Alfa AF: 0.105 Hom.: 2229

Bravo AF: 0.0816

Asia WGS AF: 0.232 AC: 806 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	0.95
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884136; hg19: chr20-10850464;