rs4389663

Positions:

• chr5-105087983-A-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.105087983A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251574	ENST00000503650.1	n.211-201008T>A		intron_variant		3
ENSG00000253584	ENST00000522464.1	n.69-79072T>A		intron_variant		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

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.754

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;