rs17065395

chr5-165622374-C-T

Variant summary

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

The ENST00000522189.1(ENSG00000253693):n.22-155603C>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 0.0861 in 152,228 control chromosomes in the GnomAD database, including 932 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 0.086 (932 hom., cov: 32)
• Consequence: ENST00000522189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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
	ENST00000522189.1	n.22-155603C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13104 AN: 152110 Hom.: 933 Cov.: 32

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0861 AC: 13103 AN: 152228 Hom.: 932 Cov.: 32 AF XY: 0.0892 AC XY: 6636 AN XY: 74416

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0934

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0827 Hom.: 85

Bravo AF: 0.0859

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	6.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17065395; hg19: chr5-165049379;