rs1390669

Positions:

• chr5-21631495-A-G

Variant summary

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

The ENST00000522350.1(ENSG00000253766):​n.476+7385A>G 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 0.0823 in 152,196 control chromosomes in the GnomAD database, including 588 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 0.082 (588 hom., cov: 33)
• Consequence: ENST00000522350.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374685	XR_925848.3	n.3830+7385A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522350.1	n.476+7385A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12505 AN: 152078 Hom.: 589 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00655

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0823 AC: 12519 AN: 152196 Hom.: 588 Cov.: 33 AF XY: 0.0798 AC XY: 5942 AN XY: 74434

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0698

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0545

Gnomad4 NFE AF: 0.0741

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0737 Hom.: 211

Bravo AF: 0.0841

Asia WGS AF: 0.0310 AC: 107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1390669; hg19: chr5-21631604;