rs2301237

Variant names:

• chr18-59779197-G-A
• rs2301237

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 0.34 in 152,174 control chromosomes in the GnomAD database, including 9,030 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 0.34 (9030 hom., cov: 33)
• Consequence: GLUD1P4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 3 publications found

Genes affected

GLUD1P4 (HGNC:4339): (glutamate dehydrogenase 1 pseudogene 4)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLUD1P4		n.59779197G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLUD1P4	ENST00000590914.1	n.*208G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51669 AN: 152056 Hom.: 9031 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.340 AC: 51684 AN: 152174 Hom.: 9030 Cov.: 33 AF XY: 0.341 AC XY: 25382 AN XY: 74392

African (AFR) AF: 0.279 AC: 11575 AN: 41506

American (AMR) AF: 0.335 AC: 5118 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5182

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4824

European-Finnish (FIN) AF: 0.391 AC: 4142 AN: 10592

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25068 AN: 67982

Other (OTH) AF: 0.351 AC: 743 AN: 2114

Alfa AF: 0.372 Hom.: 5598

Bravo AF: 0.333

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.76
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2301237; hg19: chr18-57446429;