chr8-18323583-A-G

Variant names:

• chr8-18323583-A-G
• rs13259523

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 99 gene

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

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

African (AFR) AF: 0.00740 AC: 307 AN: 41508

American (AMR) AF: 0.0191 AC: 292 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5160

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4818

European-Finnish (FIN) AF: 0.0385 AC: 408 AN: 10598

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0463 AC: 3151 AN: 68012

Other (OTH) AF: 0.0209 AC: 44 AN: 2110

Alfa AF: 0.0429 Hom.: 269

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs13259523; hg19: chr8-18181092;