chr5-105087983-A-T

Variant names:

• chr5-105087983-A-T
• rs4389663
• ENST00000503650.1:n.211-201008T>A

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.211-201008T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,132 control chromosomes in the GnomAD database, including 44,510 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 0.76 (44510 hom., cov: 33)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 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
ENSG00000251574	ENST00000503650.1	n.211-201008T>A		intron_variant	Intron 1 of 2	3
ENSG00000253584	ENST00000522464.1	n.69-79072T>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114937 AN: 152014 Hom.: 44481 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.756 AC: 115019 AN: 152132 Hom.: 44510 Cov.: 33 AF XY: 0.757 AC XY: 56267 AN XY: 74362

Gnomad4 AFR AF: 0.681 AC: 0.681336 AN: 0.681336

Gnomad4 AMR AF: 0.714 AC: 0.713996 AN: 0.713996

Gnomad4 ASJ AF: 0.793 AC: 0.792676 AN: 0.792676

Gnomad4 EAS AF: 0.286 AC: 0.286157 AN: 0.286157

Gnomad4 SAS AF: 0.714 AC: 0.71393 AN: 0.71393

Gnomad4 FIN AF: 0.890 AC: 0.889507 AN: 0.889507

Gnomad4 NFE AF: 0.825 AC: 0.824981 AN: 0.824981

Gnomad4 OTH AF: 0.754 AC: 0.753795 AN: 0.753795

Alfa AF: 0.808 Hom.: 6229

Bravo AF: 0.734

Asia WGS AF: 0.570 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4389663; hg19: chr5-104423684;