rs4598283

chr8-115916875-T-C

Variant summary

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

The XR_001745736.2(LOC107986902):n.3385T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,250 control chromosomes in the GnomAD database, including 2,474 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 0.14 (2474 hom., cov: 32)
• Consequence: LOC107986902 XR_001745736.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

LOC107986902 (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 (AMR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986902	XR_001745736.2	n.3385T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21851 AN: 152132 Hom.: 2464 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.144 AC: 21887 AN: 152250 Hom.: 2474 Cov.: 32 AF XY: 0.147 AC XY: 10979 AN XY: 74436

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.132

Alfa AF: 0.104 Hom.: 165

Bravo AF: 0.167

Asia WGS AF: 0.187 AC: 650 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	3.9
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4598283; hg19: chr8-116929100;