rs16944011

Variant names:

• chr18-27712399-C-G
• rs16944011

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0892 AC: 3705 AN: 41538

American (AMR) AF: 0.0576 AC: 879 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3470

East Asian (EAS) AF: 0.0496 AC: 256 AN: 5166

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4826

European-Finnish (FIN) AF: 0.0328 AC: 347 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0668 AC: 4542 AN: 67964

Other (OTH) AF: 0.0773 AC: 163 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs16944011; hg19: chr18-25292363;