18-31619216-T-C

Variant names:

• chr18-31619216-T-C
• rs1621308

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 0.374 in 151,552 control chromosomes in the GnomAD database, including 10,744 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 0.37 (10744 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.374 AC: 56638 AN: 151436 Hom.: 10732 Cov.: 30

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.374 AC: 56698 AN: 151552 Hom.: 10744 Cov.: 30 AF XY: 0.372 AC XY: 27541 AN XY: 74038

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.380

Alfa AF: 0.326 Hom.: 3746

Bravo AF: 0.384

Asia WGS AF: 0.320 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.074
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1621308; hg19: chr18-29199179;