18-31619216-T-C

Variant names:

• chr18-31619216-T-C
• rs1621308

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 0.374 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.426 AC: 17580 AN: 41264

American (AMR) AF: 0.372 AC: 5669 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1531 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2054 AN: 5146

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4814

European-Finnish (FIN) AF: 0.328 AC: 3434 AN: 10462

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23706 AN: 67858

Other (OTH) AF: 0.380 AC: 797 AN: 2100

Alfa AF: 0.353 Hom.: 7271

Bravo AF: 0.384

Asia WGS AF: 0.320 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.074
DANN	Benign	0.50
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1621308; hg19: chr18-29199179;