rs1995138

Variant names:

• chr18-54000198-G-A
• rs1995138

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 0.165 in 147,636 control chromosomes in the GnomAD database, including 3,554 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 0.17 (3554 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 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: 0.165 AC: 24347 AN: 147524 Hom.: 3543 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00144

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.165 AC: 24398 AN: 147636 Hom.: 3554 Cov.: 31 AF XY: 0.163 AC XY: 11684 AN XY: 71670

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.00144

Gnomad4 SAS AF: 0.0550

Gnomad4 FIN AF: 0.0826

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0900 Hom.: 1374

Bravo AF: 0.173

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1995138; hg19: chr18-51526568;