rs9959259

Variant names:

• chr18-75838008-G-A
• rs9959259

Your query was ambiguous. Multiple possible variants found:

• chr18-75838008-G-A
• chr18-75838008-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.303 in 152,038 control chromosomes in the GnomAD database, including 8,048 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 0.30 (8048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

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: 0.303 AC: 46079 AN: 151920 Hom.: 8044 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.303 AC: 46105 AN: 152038 Hom.: 8048 Cov.: 32 AF XY: 0.296 AC XY: 22010 AN XY: 74310

African (AFR) AF: 0.170 AC: 7032 AN: 41484

American (AMR) AF: 0.252 AC: 3845 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3466

East Asian (EAS) AF: 0.0418 AC: 216 AN: 5172

South Asian (SAS) AF: 0.275 AC: 1322 AN: 4816

European-Finnish (FIN) AF: 0.321 AC: 3388 AN: 10542

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27739 AN: 67970

Other (OTH) AF: 0.296 AC: 625 AN: 2114

Alfa AF: 0.367 Hom.: 32409

Bravo AF: 0.290

Asia WGS AF: 0.159 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.27
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9959259; hg19: chr18-73549963;