rs4520160

Variant names:

• chr8-22704371-G-A
• rs4520160
• ENST00000523627.1:n.164+14058G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-22704371-G-A
• chr8-22704371-G-C

Variant summary

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

The ENST00000523627.1(ENSG00000253125):​n.164+14058G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 121,250 control chromosomes in the GnomAD database, including 11,962 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 0.49 (11962 hom., cov: 29)
• Consequence: ENSG00000253125 ENST00000523627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

ENSG00000253125 (HGNC:58186):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 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
ENSG00000253125	ENST00000523627.1	n.164+14058G>A		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.493 AC: 59774 AN: 121158 Hom.: 11940 Cov.: 29

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.492

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.493 AC: 59831 AN: 121250 Hom.: 11962 Cov.: 29 AF XY: 0.494 AC XY: 29250 AN XY: 59260

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.520

Alfa AF: 0.377 Hom.: 5307

Bravo AF: 0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4520160; hg19: chr8-22561884;