rs34886602

Positions:

• chr18-57590297-C-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 0.0787 in 152,110 control chromosomes in the GnomAD database, including 937 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 0.079 (937 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57590297C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11961 AN: 151988 Hom.: 932 Cov.: 33

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.00991

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0787 AC: 11978 AN: 152110 Hom.: 937 Cov.: 33 AF XY: 0.0864 AC XY: 6424 AN XY: 74340

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.0989

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.0740

Alfa AF: 0.0736 Hom.: 82

Bravo AF: 0.0850

Asia WGS AF: 0.199 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34886602; hg19: chr18-55257529;