rs2019441

Variant names:

• chr18-25617916-T-C
• rs2019441

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0393 in 152,170 control chromosomes in the GnomAD database, including 179 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 0.039 (179 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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: 0.0393 AC: 5980 AN: 152052 Hom.: 179 Cov.: 33

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0343

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0393 AC: 5983 AN: 152170 Hom.: 179 Cov.: 33 AF XY: 0.0414 AC XY: 3082 AN XY: 74400

African (AFR) AF: 0.0258 AC: 1072 AN: 41556

American (AMR) AF: 0.0659 AC: 1007 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3468

East Asian (EAS) AF: 0.143 AC: 728 AN: 5108

South Asian (SAS) AF: 0.102 AC: 493 AN: 4818

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10622

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0343 AC: 2332 AN: 68000

Other (OTH) AF: 0.0407 AC: 86 AN: 2114

Alfa AF: 0.0356 Hom.: 203

Bravo AF: 0.0407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	19
DANN	Benign	0.73
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs2019441; hg19: chr18-23197880;