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. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000253125 (HGNC:58186):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.427 AC: 15103 AN: 35394

American (AMR) AF: 0.598 AC: 7570 AN: 12668

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1456 AN: 2984

East Asian (EAS) AF: 0.351 AC: 1421 AN: 4048

South Asian (SAS) AF: 0.479 AC: 1642 AN: 3428

European-Finnish (FIN) AF: 0.500 AC: 4061 AN: 8116

Middle Eastern (MID) AF: 0.496 AC: 115 AN: 232

European-Non Finnish (NFE) AF: 0.524 AC: 27294 AN: 52110

Other (OTH) AF: 0.520 AC: 863 AN: 1660

Alfa AF: 0.378 Hom.: 6972

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
PhyloP100		-1.7
Mutation Taster		=60/40	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4520160; hg19: chr8-22561884;