rs1893220

Variant names:

• chr18-13916295-G-T
• rs1893220

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 0.355 in 152,068 control chromosomes in the GnomAD database, including 10,563 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 (10563 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 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: 0.355 AC: 53997 AN: 151950 Hom.: 10565 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.355 AC: 54008 AN: 152068 Hom.: 10563 Cov.: 33 AF XY: 0.356 AC XY: 26414 AN XY: 74298

African (AFR) AF: 0.210 AC: 8722 AN: 41516

American (AMR) AF: 0.342 AC: 5221 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1107 AN: 5172

South Asian (SAS) AF: 0.236 AC: 1136 AN: 4822

European-Finnish (FIN) AF: 0.504 AC: 5307 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29754 AN: 67966

Other (OTH) AF: 0.370 AC: 780 AN: 2108

Alfa AF: 0.387 Hom.: 1564

Bravo AF: 0.339

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.72
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1893220; hg19: chr18-13916294;