4-170592586-C-A

Position:

• chr4-170592586-C-A

Variant summary

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

The ENST00000325407.4(ENSG00000293021):​n.189-10999G>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 0.529 in 152,020 control chromosomes in the GnomAD database, including 24,686 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 0.53 (24686 hom., cov: 32)
• Consequence: ENST00000325407.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000325407.4	n.189-10999G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80414 AN: 151902 Hom.: 24683 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.529 AC: 80442 AN: 152020 Hom.: 24686 Cov.: 32 AF XY: 0.537 AC XY: 39895 AN XY: 74306

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.538

Alfa AF: 0.626 Hom.: 38017

Bravo AF: 0.493

Asia WGS AF: 0.743 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs368771; hg19: chr4-171513737;