18-31619216-T-C

Position:

• chr18-31619216-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;