rs4520160

Positions:

• 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, non coding transcript 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: ENST00000523627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523627.1	n.164+14058G>A		intron_variant, non_coding_transcript_variant		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;