rs16944011

Positions:

• chr18-27712399-C-G

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 0.0685 in 152,146 control chromosomes in the GnomAD database, including 370 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 0.068 (370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0868 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: 0.0685 AC: 10414 AN: 152028 Hom.: 368 Cov.: 32

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0576

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0685 AC: 10421 AN: 152146 Hom.: 370 Cov.: 32 AF XY: 0.0659 AC XY: 4898 AN XY: 74374

Gnomad4 AFR AF: 0.0892

Gnomad4 AMR AF: 0.0576

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0496

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.0328

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.0773

Alfa AF: 0.0698 Hom.: 53

Bravo AF: 0.0724

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16944011; hg19: chr18-25292363;