rs13259523

chr8-18323583-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0297 in 152,140 control chromosomes in the GnomAD database, including 99 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 0.030 (99 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0297 (4518/152140) while in subpopulation NFE AF= 0.0463 (3151/68012). AF 95% confidence interval is 0.045. There are 99 homozygotes in gnomad4. There are 2183 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 99 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0297 AC: 4517 AN: 152024 Hom.: 99 Cov.: 32

Gnomad AFR AF: 0.00742

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0253

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0297 AC: 4518 AN: 152140 Hom.: 99 Cov.: 32 AF XY: 0.0294 AC XY: 2183 AN XY: 74378

Gnomad4 AFR AF: 0.00740

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0255

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.0463

Gnomad4 OTH AF: 0.0209

Alfa AF: 0.0394 Hom.: 48

Bravo AF: 0.0265

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
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: rs13259523; hg19: chr8-18181092;