rs1858378

Variant names:

• chr18-38277474-G-A
• rs1858378

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 0.358 in 151,732 control chromosomes in the GnomAD database, including 10,335 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 0.36 (10335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.358 AC: 54318 AN: 151614 Hom.: 10326 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.358 AC: 54372 AN: 151732 Hom.: 10335 Cov.: 32 AF XY: 0.357 AC XY: 26456 AN XY: 74124

African (AFR) AF: 0.495 AC: 20501 AN: 41382

American (AMR) AF: 0.333 AC: 5055 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2361 AN: 5116

South Asian (SAS) AF: 0.275 AC: 1320 AN: 4808

European-Finnish (FIN) AF: 0.280 AC: 2949 AN: 10544

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19744 AN: 67912

Other (OTH) AF: 0.366 AC: 769 AN: 2100

Alfa AF: 0.314 Hom.: 12898

Bravo AF: 0.372

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.2
DANN	Benign	0.48
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1858378; hg19: chr18-35857438;