rs299384

Variant names:

• chr5-17368063-G-A
• rs299384
• ENST00000653016.1:n.810C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-17368063-G-A
• chr5-17368063-G-C
• 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: ENSG00000249199 ENST00000653016.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

ENSG00000249199 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249199	ENST00000653016.1	n.810C>T		non_coding_transcript_exon_variant	Exon 3 of 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;