rs1568237

Positions:

• chr18-68100995-G-A

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 0.545 in 151,826 control chromosomes in the GnomAD database, including 23,162 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 0.55 (23162 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82689 AN: 151706 Hom.: 23114 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.545 AC: 82799 AN: 151826 Hom.: 23162 Cov.: 31 AF XY: 0.546 AC XY: 40519 AN XY: 74214

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.554

Alfa AF: 0.518 Hom.: 8610

Bravo AF: 0.564

Asia WGS AF: 0.750 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1568237; hg19: chr18-65768232;