rs870391

Variant names:

• chr18-38305841-C-T
• rs870391

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.347 in 152,002 control chromosomes in the GnomAD database, including 9,406 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 0.35 (9406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 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: 0.347 AC: 52726 AN: 151882 Hom.: 9398 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.347 AC: 52767 AN: 152002 Hom.: 9406 Cov.: 32 AF XY: 0.346 AC XY: 25705 AN XY: 74286

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.360

Alfa AF: 0.318 Hom.: 16117

Bravo AF: 0.358

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.047
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs870391; hg19: chr18-35885805;