rs1450822

Positions:

• chr5-4520743-G-A
• chr5-4520743-G-C
• chr5-4520743-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000507435.1(ENSG00000248973):​n.532+1522C>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 0.442 in 151,862 control chromosomes in the GnomAD database, including 15,493 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 0.44 (15493 hom., cov: 33)
• Consequence: ENST00000507435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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
	ENST00000507435.1	n.532+1522C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67016 AN: 151744 Hom.: 15485 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.442 AC: 67052 AN: 151862 Hom.: 15493 Cov.: 33 AF XY: 0.441 AC XY: 32727 AN XY: 74194

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.456

Alfa AF: 0.488 Hom.: 36942

Bravo AF: 0.439

Asia WGS AF: 0.462 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	13
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1450822; hg19: chr5-4520856;