5-165656790-C-T

Variant names:

• chr5-165656790-C-T
• rs262714
• ENST00000522189.1:n.22-121187C>T

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.22-121187C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,030 control chromosomes in the GnomAD database, including 34,953 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 0.67 (34953 hom., cov: 32)
• Consequence: ENSG00000253693 ENST00000522189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

ENSG00000253693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 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
ENSG00000253693	ENST00000522189.1	n.22-121187C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102399 AN: 151912 Hom.: 34924 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.674 AC: 102480 AN: 152030 Hom.: 34953 Cov.: 32 AF XY: 0.676 AC XY: 50226 AN XY: 74290

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.645

Alfa AF: 0.620 Hom.: 28569

Bravo AF: 0.682

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs262714; hg19: chr5-165083795;