rs2194189

Variant names:

• chr16-15205360-C-T
• rs2194189
• ENST00000737633.1:n.83-43532G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000737633.1(ENSG00000296252):​n.83-43532G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.056 (355 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000296252 ENST00000737633.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 1 publications found

Genes affected

ENSG00000296252 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737633.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000296252	ENST00000737633.1		n.83-43532G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8134 AN: 146414 Hom.: 355 Cov.: 27

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.0200

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0117

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.0260

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0494

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0556 AC: 8144 AN: 146534 Hom.: 355 Cov.: 27 AF XY: 0.0574 AC XY: 4102 AN XY: 71474

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0382 AC: 1545 AN: 40440

American (AMR) AF: 0.0813 AC: 1178 AN: 14484

Ashkenazi Jewish (ASJ) AF: 0.0117 AC: 40 AN: 3414

East Asian (EAS) AF: 0.172 AC: 789 AN: 4574

South Asian (SAS) AF: 0.0681 AC: 308 AN: 4524

European-Finnish (FIN) AF: 0.0776 AC: 781 AN: 10064

Middle Eastern (MID) AF: 0.0278 AC: 8 AN: 288

European-Non Finnish (NFE) AF: 0.0513 AC: 3374 AN: 65800

Other (OTH) AF: 0.0504 AC: 103 AN: 2044

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0762 Hom.: 59

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.52
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2194189; hg19: chr16-15299217;