rs1450822

Variant names:

• chr5-4520743-G-A
• rs1450822
• ENST00000507435.1:n.532+1522C>T

Your query was ambiguous. Multiple possible variants found:

• 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 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: ENSG00000248973 ENST00000507435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

ENSG00000248973 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248973	ENST00000507435.1	n.532+1522C>T		intron_variant	Intron 4 of 5	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;