rs2019441

Variant names:

• chr18-25617916-T-C
• rs2019441

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0343

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0352 Hom.: 145

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2019441; hg19: chr18-23197880;