chr4-177584042-A-T

Variant names:

• chr4-177584042-A-T
• rs4234867
• ENST00000507023.1:n.582-9430A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507023.1(AGA-DT):​n.582-9430A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,996 control chromosomes in the GnomAD database, including 19,691 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 (19691 hom., cov: 32)
• Consequence: AGA-DT ENST00000507023.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725

Genes affected

AGA-DT (HGNC:27730): (AGA divergent transcript)

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 (SAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGA-DT	NR_183777.1	n.551-12419A>T		intron_variant	Intron 2 of 4
AGA-DT	NR_183778.1	n.435-12419A>T		intron_variant	Intron 1 of 5
AGA-DT	NR_183779.1	n.435-12419A>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGA-DT	ENST00000507023.1	n.582-9430A>T		intron_variant	Intron 2 of 5	2
AGA-DT	ENST00000654463.1	n.64-9430A>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73857 AN: 151878 Hom.: 19676 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.486 AC: 73904 AN: 151996 Hom.: 19691 Cov.: 32 AF XY: 0.488 AC XY: 36287 AN XY: 74298

Gnomad4 AFR AF: 0.249 AC: 0.249458 AN: 0.249458

Gnomad4 AMR AF: 0.557 AC: 0.557455 AN: 0.557455

Gnomad4 ASJ AF: 0.605 AC: 0.604671 AN: 0.604671

Gnomad4 EAS AF: 0.507 AC: 0.507193 AN: 0.507193

Gnomad4 SAS AF: 0.647 AC: 0.646888 AN: 0.646888

Gnomad4 FIN AF: 0.525 AC: 0.525185 AN: 0.525185

Gnomad4 NFE AF: 0.587 AC: 0.586667 AN: 0.586667

Gnomad4 OTH AF: 0.564 AC: 0.563628 AN: 0.563628

Alfa AF: 0.526 Hom.: 2757

Bravo AF: 0.478

Asia WGS AF: 0.566 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4234867; hg19: chr4-178505196;