rs299384

Positions:

• chr5-17368063-G-A
• chr5-17368063-G-T

Variant summary

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

The ENST00000653016.1(ENSG00000249199):​n.810C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,064 control chromosomes in the GnomAD database, including 1,058 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 0.11 (1058 hom., cov: 31)
• Consequence: ENST00000653016.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653016.1	n.810C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17434 AN: 151944 Hom.: 1058 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.115 AC: 17448 AN: 152064 Hom.: 1058 Cov.: 31 AF XY: 0.115 AC XY: 8548 AN XY: 74320

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0737

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0927

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.107

Alfa AF: 0.105 Hom.: 1231

Bravo AF: 0.112

Asia WGS AF: 0.118 AC: 412 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	0.11
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs299384; hg19: chr5-17368172;