chr5-165622374-C-T

Variant names:

• chr5-165622374-C-T
• rs17065395
• ENST00000522189.1:n.22-155603C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522189.1(ENSG00000253693):​n.22-155603C>T variant causes a intron 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: ENSG00000253693 ENST00000522189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 0 publications found

Genes affected

ENSG00000253693 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522189.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253693	ENST00000522189.1	TSL:5	n.22-155603C>T		intron	N/A

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

African (AFR) AF: 0.0196 AC: 814 AN: 41552

American (AMR) AF: 0.115 AC: 1753 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1444 AN: 5158

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4822

European-Finnish (FIN) AF: 0.0650 AC: 690 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0934 AC: 6351 AN: 68020

Other (OTH) AF: 0.0818 AC: 173 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17065395; hg19: chr5-165049379;